Biomedical subjects

Yang Song

Publications and source records attributed to Yang Song.

At least 19 recordsLinked to original sources

PubMed2026

Ecological Filtering by Tuber Compartments Shapes Stable Core Microbiomes That Underpin Potato Plant Growth Across Environments.

Harnessing plant microbiomes for sustainable agriculture requires understanding not only whether they can boost crop performance, but also how ecological processes govern their assembly, stability, and functional contributions across environments. While we previously showed that seed tuber microbiomes can predict potato vigour using machine learning, it remained unclear how ecological processes shape tuber microbiome stability and functionality across host genotypes, tuber compartments, soil types, and years. Here, we analyzed the national-scale dataset of 240 field-collected potato seedlots, spanning six genotypes, two soil types, and two growing years, with a focus on the spatially distinct heel and eye compartments of the potato tuber. By profiling over 1200 bacterial and fungal communities and linking microbiome composition to plant performance, we show that plant genotype and tuber compartment are the strongest determinants of microbial diversity and composition. Compartment-specific enrichment of functional traits revealed spatial partitioning of microbial functions, with organic compound conversion and nitrogen cycling dominant in the heel, and energy metabolism enriched in the eye. Applying a macroecological abundance-occupancy framework, we identified a stable core microbiome of bacterial and fungal taxa that persisted across all environments and years. These core members were more strongly associated with plant growth-related traits than non-core taxa, and core taxa in different tuber compartments showed distinct correlations with taxa of potential pathogenic relevance. Together, our findings demonstrate that tuber compartments act as ecological filters that structure persistent, functionally specialised microbiomes linked to plant growth-related traits across environments. By providing an ecological and functional framework for compartment-resolved, stable core microbiomes, this study advances mechanistic understanding of plant-microbe interactions and identifies stable microbial partners as promising targets for improving potato resilience and productivity.

Journal Article↗

PubMed2026

TNIK Overexpression Is Sufficient for Chemoradiation Resistance in Limited-Stage Small Cell Lung Cancer.

Small cell lung cancer (SCLC) is characterized by early metastasis, intrinsic chemoradiation resistance, and tumor recurrence. Besides the lack of potentially targetable oncogenic drivers, therapeutic advancements are also hindered by the scarcity of surgically resected tissue specimens ideal for profiling studies. We used patient-derived xenografts (PDX) to model SCLC chemoradiation resistance and identified chemoradiation resistance candidate genes using RNA sequencing. Additionally, we used human SCLC cell lines to confirm our in vivo results and delineate the underlying mechanism. Transcriptome profiling showed that the Traf2- and Nck-interacting kinase (TNIK) gene was consistently upregulated in an array of SCLC PDXs exposed to chemoradiation compared with monotherapy, which is consistent with previous observations of TNIK amplification in human samples. Genetic depletion (P < 0.01) or pharmacologic inhibition (P < 0.0001) of TNIK reduced in vitro clonogenic survival of TNIKhigh SCLC cells and promoted sensitivity to chemoradiation. In vivo, pharmacologic inhibition of TNIK enhanced chemoradiation sensitivity (P < 0.0001) of the H446 cell line-derived xenograft (CDX) in NOD-SCID mice. Furthermore, pharmacologic inhibition of TNIK in vivo demonstrated sensitivity (P < 0.0001) to chemoradiotherapy (CRT) in LX33 PDX. These results indicate that TNIK plays a role in conferring resistance to chemoradiation in SCLC cell lines and in vivo in SCLC CDX and PDX models. Delineating the mechanism behind radiosensitization suggested that TNIK inhibition may impair the DNA damage response in irradiated cells. Collectively, these findings suggest that TNIK may be a promising therapeutic target in limited-stage SCLC and support further investigation of TNIK inhibition in combination with standard CRT.

Humans↗

PubMed2026

Machine Learning-Based Preoperative Predicting TERT Promoter Mutation and EGFR Gene Amplification Phenotype in IDH Wild-Type Glioblastoma Using Advanced MR Habitat Imaging.

BACKGROUND AND PURPOSE: The telomerase reverse transcriptase (TERT) gene promoter mutation is a crucial factor for identifying an isocitrate dehydrogenase (IDH) wild-type glioblastoma with poor prognosis, and the epidermal growth factor receptor (EGFR) amplification may be a potential prognostic factor. The purpose of this study was to investigate the value of the tumor habitats imaging model on advanced MRI in predicting TERT promoter mutation and EGFR gene amplification phenotype of IDH wild-type glioblastoma. MATERIALS AND METHODS: One hundred seventy-nine patients with pretreatment conventional MRI, DWI, and DSC-PWI were included. The data were divided into the training set (n=112), test set (n=29), and time-independent validation set (n=38). Based on the ADC and CBV map, the solid tumor area was split into several habitat subregions using the k-means clustering algorithm (hypovascular hypercellular area, hypervascular area, and hypovascular hypocellular area). In the training set, TERT promoter mutation and EGFR gene amplification phenotype prediction models were constructed using the random forest method. The reliability of prediction models was validated in the test and the time-independent validation sets. Receiver operating characteristic (ROC) curve analysis, calibration curve, and decision curve analysis (DCA) were used. RESULTS: The area under the curve (AUC) of the training, test, and validation sets of the TERT promoter prediction model was 0.877, 0.783, and 0.796, respectively. The accuracy of the TERT promoter prediction model was 82.1%, 75.9%, and 76.3%, respectively. The AUCs of the 3 sets for the EGFR gene amplification status prediction model were 0.877, 0.784, and 0.878, respectively. The accuracy of the EGFR gene amplification status prediction model was 79.5%, 75.9%, and 89.5%, respectively. Moreover, the prediction probability of these models was in good agreement with the actual result. CONCLUSIONS: The tumor habitat imaging model based on advanced MRI was useful for accurately predicting TERT promoter mutation and EGFR amplification status in IDH wild-type glioblastoma.

Humans↗

PubMed2025

Immunosuppressants Rewire the Gut Microbiome-Alloimmune Axis Through Time-Dependent and Tissue-Specific Mechanisms.

BACKGROUND: Lifelong immunosuppressive therapy is required to prevent allograft rejection in organ transplantation. Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in severe off-target complications. It remains a significant unmet medical need in transplant medicine. RESULTS: In this study we investigated immunosuppressant effects of four major immunosuppressant classes, including tacrolimus, prednisone, mycophenolate mofetil (MMF), and fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking after up to 30-day chronic exposure. Despite their distinct mechanisms of action and not designed to target the gut, all immunosuppressive drugs induced profound and time-dependent alterations in both intestine gene expression and gut microbiome composition. Progressive alterations from moderate early, drug-specific changes to a strikingly convergent microbial dysbiosis, marked by significant expansion of pathobionts of Muribaculaceae, occurred across all drug classes. Concurrently, all drugs uniformly induced significant suppression of mucosal immunity including B cell, immunoglobulin, and antigen recognition. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, marked by a progressive shift toward pro-inflammatory phenotypes in gut-draining mesenteric LNs and a gradual loss of tolerogenic architecture in peripheral LNs. Drug-specific metabolic alterations and distinct phases of intestinal transcriptional responses were also characterized. Notably, MMF and FTY demonstrated the most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cell distribution and LN remodeling. CONCLUSIONS: Together, these findings highlight the underappreciated complexity and temporal dynamics immunosuppressants effects, particularly their impact on the gut and compartmentalized regulation of alloimmune in lymphoid tissues. Understanding these relationships offers new opportunities for refining immunosuppressive strategies to reduce treatment-related off-target complications and improve long-term organ transplant outcomes.

gut dysbiosis↗

PubMed2023

Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum.

The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.

Mice↗

PubMed2007

Self-scheduling for hospital nurses: an attempt and its difficulties.

AIM: To describe a pilot project on self-scheduling (self-rostering) for hospital nurses and assess its potential values and difficulties in implementation. BACKGROUND: Self-scheduling is one aspect of the effort to make the hospital nursing environment more accommodative of nurses' lives. It is part of the good employment practices that nurses want and that can help recruitment, retention and--possibly--patient care. METHOD: A self-scheduling programme was implemented on one nursing floor for a year. Its effect on nursing perceptions was gauged by an informal questionnaire, and its effect on the nurse manager was gauged by counting change requests and sick calls, as well as her time spent on scheduling and her perceived annoyance in doing it. FINDINGS: During the time of the pilot project nurses felt that they had better control of their time and were able to give better patient care. Also, change requests decreased, as did the time spent by the nurse manager and her sense of annoyance. But since the nurses did not adhere to the rules of the programme, despite repeated efforts by the nurse manager, the attempt floundered. CONCLUSION: Self-scheduling can have positive results for nurses and benefit the nurse manager. But if nurses see this as an individual entitlement instead of a balance between individual and unit benefit, everyone loses. This experience may be of use to others trying to implement a self-scheduling system.

Absenteeism↗

PubMed2006

Dietary zinc restriction in rats alters antioxidant status and increases plasma F2 isoprostanes.

Approximately 12% of Americans do not consume the estimated average requirement for zinc and could be at risk for zinc deficiency. Since zinc has proposed antioxidant function, inadequate zinc consumption may lead to an enhanced susceptibility to oxidative stress through several mechanisms, including altered antioxidant defenses. In this study, we hypothesized that dietary zinc restriction would result in lower antioxidant status and increased oxidative damage. We fed weanling Sprague-Dawley rats (n=12 per group) a zinc-adequate (50 mg/kg of zinc) diet, a zinc-deficient (<0.05 mg/kg of zinc) diet or a pair-fed diet for 3 weeks and then assessed their antioxidant status and oxidative stress parameters. Rats were zinc deficient as indicated by a significant (P<.05) reduction in body weight (49%) and 19% lower (P<.05) hepatic zinc (20.6+/-2.1 mg/kg) as compared with zinc-adequate rats (24.6+/-2.2 mg/kg). Zinc deficiency resulted in elevated (P<.05) plasma F(2) isoprostanes. Zinc deficiency-mediated oxidative stress was accompanied by a 20% decrease (P<.05) in the ferritin-reducing ability of plasma assay and a 50% reduction in plasma uric acid (P<.05). No significant change in plasma ascorbic acid or in plasma alpha-tocopherol and gamma-tocopherol was observed. However, hepatic alpha-tocopherol and gamma-tocopherol concentrations were decreased by 38% and 27% (P<.05), respectively, as compared with those in zinc-adequate rats. Hepatic alpha-tocopherol transfer protein levels were unaltered (P>.05) by zinc deficiency, but cytochrome P450 (CYP) 4F2 protein levels were elevated (P<.05) as compared with those in zinc-adequate rats. Collectively, zinc deficiency increased oxidative stress, which may be partially explained by increased CYP activity and reductions in hepatic alpha-tocopherol and gamma-tocopherol and in plasma uric acid.

Animals↗

PubMed2006

Algebraic iterative algorithm for deflection tomography and its application to density flow fields in a hypersonic wind tunnel.

A novel algebraic iterative algorithm based on deflection tomography is presented. This algorithm is derived from the essentials of deflection tomography with a linear expansion of the local basis functions. By use of this algorithm the tomographic problem is finally reduced to the solution of a set of linear equations. The algorithm is demonstrated by mapping a three-peak Gaussian simulative temperature field. Compared with reconstruction results obtained by other traditional deflection algorithms, its reconstruction results provide a significant improvement in reconstruction accuracy, especially in cases with noisy data added. In the density diagnosis of a hypersonic wind tunnel, this algorithm is adopted to reconstruct density distributions of an axial symmetry flow field. One cross section of the reconstruction results is selected to be compared with the inverse Abel transform algorithm. Results show that the novel algorithm can achieve an accuracy equivalent to the inverse Abel transform algorithm. However, the novel algorithm is more versatile because it is applicable to arbitrary kinds of distribution.

Journal Article↗

PubMed2006

Development of an efficient method for the preparative isolation and purification of chlorophyll a from a marine dinoflagellate Amphidinium carterae by high-speed counter-current chromatography coupled with reversed-phase high-performance liquid chromatography.

In our research into chlorophylls of marine dinoflagellates, chlorophyll a was separated rapidly from the hexane extract of Amphidinium carterae in three steps. The first step was silica gel column chromatography, where elution was performed with 0-50% ethyl acetate in n-hexane. The second was high-speed counter-current chromatography using a two-phase solvent system consisting of n-hexane-ethyl acetate-methanol-water (5:5:5:1, v/v), and the third step was preparative reversed-phase high-performance liquid chromatography using a solvent system of acetone-water (89:11, v/v). HPLC analysis showed that the purity of chlorophyll a from the second step was over 83%, and after the third it was over 99%. Thirty milligrams of chlorophyll a was isolated from a crude sample of 250 mg of chlorophylls, and its structure was identified by analyzing its MS, 1H NMR and 13C NMR spectra.

Animals↗

PubMed2006

Establishment of a functional ovine fetoplacental artery endothelial cell line with a prolonged life span.

To study mechanisms governing fetoplacental vascular function, we have established a primary ovine fetoplacental artery endothelial (OFPAE) cell line. These OFPAE cells produce nitric oxide (NO), proliferate, and migrate in response to fibroblast growth factor 2 (FGF2) and vascular endothelial growth factor (VEGF). To overcome the senescence crisis that this primary OFPAE cell line will eventually enter, we attempted to establish a functional OFPAE cell line with a prolonged life span by transfecting cells with plasmids containing a neomycin resistance gene and a simian virus 40 gene (SV40) expressing large T (T) and small t (t) antigens. The OFPAE cells at passage 8 were transfected. After neomycin selection, the surviving OFPAE (designated SV40 OFPAE) cells were expanded up to passage 80. Up to passage 30, these SV40 OFPAE cells maintained a morphology similar to untransfected OFPAE cells. Expression of T and t antigens in SV40 OFPAE cells was confirmed by immunocytochemistry. These SV40 OFPAE cells exhibited positive uptake of acetylated low-density lipoprotein (Ac-LDL) and positive staining for NO synthase 3 (NOS3) and formed capillary-like tube structures on Matrigel. Up to passages 20-23, these SV40 OFPAE cells proliferated (P < 0.05) and produced (P < 0.05) NO in response to both FGF2 and VEGF. Moreover, this cell proliferation stimulated by FGF2 and VEGF was dose-dependently inhibited (P < 0.05) by PD98059 (a selective mitogen-activated protein kinase 1 and 2 [MAP2K1/2, also termed MEK1/2] inhibitor) or by LY294002 (a selective phosphoinositide 3-kinase [PI3K] inhibitor). These data indicate that SV40 OFPAE cells, at least at passage 23, retain endothelial phenotypes and functions similar to their parental, untransfected OFPAE cells. Thus, a functional OFPAE cell line with an extended life span has been successfully established, potentially providing a valuable cell model for studying fetoplacental endothelial function.

Animals↗

PubMed2006

Metal core bonding motifs of monodisperse icosahedral Au13 and larger Au monolayer-protected clusters as revealed by X-ray absorption spectroscopy and transmission electron microscopy.

The atomic metal core structures of the subnanometer clusters Au13[PPh3]4[S(CH2)11CH3]2Cl2 (1) and Au13[PPh3]4[S(CH2)11CH3]4 (2) were characterized using advanced methods of electron microscopy and X-ray absorption spectroscopy. The number of gold atoms in the cores of these two clusters was determined quantitatively using high-angle annular dark field scanning transmission electron microscopy. Multiple-scattering-path analyses of extended X-ray absorption fine structure (EXAFS) spectra suggest that the Au metal cores of each of these complexes adopt an icosahedral structure with a relaxation of the icosahedral strain. Data from microscopy and spectroscopy studies extended to larger thiolate-protected gold clusters showing a broader distribution in nanoparticle core sizes (183 +/- 116 Au atoms) reveal a bulklike fcc structure. These results further support a model for the monolayer-protected clusters (MPCs) in which the thiolate ligands bond preferentially at 3-fold atomic sites on the nanoparticle surface, establishing an average composition for the MPC of Au180[S(CH2)11CH3]40. Results from EXAFS measurements of a gold(I) dodecanethiolate polymer are presented that offer an alternative explanation for observations in previous reports that were interpreted as indicating Au MPC structures consisting of a Au core, Au2S shell, and thiolate monolayer.

Journal Article↗

PubMed2006

Phenol quaternary ammonium derivatives: charge and linker effect on their DNA photo-inducible cross-linking abilities.

We report here that phenol derivatives with two and four quaternary ammoniums were synthesized and their abilities to bind and cross-link DNA were investigated. Thermal denaturizing studies indicated that derivatives possess similar DNA binding abilities and gel electrophoresis revealed that more charges (series B) and electronic donation substitute linkers (like -S-) dramatically increase the DNA cross-linking abilities.

Cross-Linking Reagents↗

PubMed2006

Effects of inositol hexaphosphate on proliferation of HT-29 human colon carcinoma cell line.

AIM: To investigate the effects of inositol hexaphosphate (IP(6)) on proliferation of HT-29 human colon carcinoma cell line. METHODS: Cells were exposed to various concentrations (0, 1.8, 3.3, 5.0, 8.0, 13.0 mmol/L) of IP(6) for a certain period of time. Its effect on growth of HT-29 cells was measured by MTT assay. The expressions of cell cycle regulators treated with IP(6) for 2 d were detected by immunocytochemistry. RESULTS: IP(6) inhibited the HT-29 cell growth in a dose- and time-dependent manner. Analysis of cell cycle regulator expression revealed that IP(6) reduced the abnormal expression of P53 and PCNA and induced the expression of P21. CONCLUSION: IP(6) has potent inhibitory effect on proliferation of HT-29 cells by modulating the expression of special cell cycle regulators.

Antineoplastic Agents↗

PubMed2006

Sub-nanometer Au monolayer-protected clusters exhibiting molecule-like electronic behavior: quantitative high-angle annular dark-field scanning transmission electron microscopy and electrochemical characterization of clusters with precise atomic stoichiometry.

The synthesis and characterization of the clusters Au13[PPh3]4[S(CH2)11CH3]2Cl2 (1) and Au13[PPh3]4[S(CH2)11CH3]4 (2) are described. These mixed-ligand, sub-nanometer clusters, prepared via exchange of dodecanethiol onto phosphine-halide gold clusters, show enhanced stability relative to the parent. The characterization of these clusters features the precise determination of the number of gold atoms in the cluster cores using high-angle annular dark-field scanning transmission electron microscopy, allowing the assignment of 13 gold atoms (+/-3 atoms) to the composition of both cluster molecules. Electrochemical and optical measurements reveal discrete molecular orbital levels and apparent energy gaps of 1.6-1.7 eV for the two cluster molecules. The electrochemical measurements further indicate that the Au13[PPh3]4[S(CH2)11CH3]2Cl2 cluster undergoes an overall two-electron reduction. The electrochemical and spectroscopic properties of the two Au13 cluster molecules are compared with those of a secondary synthetic product, which proved to be larger Au thiolate-derivatized monolayer-protected clusters with an average core of Au180. The latter shows behavior fully consistent with the adoption of metallic-like properties.

Journal Article↗

PubMed2006

Pressure-induced phase transformations in LiAlH4.

The pressure-induced phase transformations in pure LiAlH4 have been studied using in situ Raman spectroscopy up to 7 GPa. The analyses of Raman spectra reveal a phase transition at approximately 3 GPa from the ambient pressure monoclinic alpha-LiAlH4 phase (P2(1)/c) to a high pressure phase (beta-LiAlH4, reported recently to be monoclinic with space group I4(1)/b) having a distorted [AlH4]- tetrahedron. The Al-H stretching mode softens and shifts dramatically to lower frequencies beyond the phase transformation pressure. The high pressure beta-LiAlH4 phase was pressure quenchable and can be recovered at lower pressures ( approximately 1.2 GPa). The Al-H stretching mode in the quenched state further shifts to lower frequencies, suggesting a weakening of the Al-H bond.

Journal Article↗

PubMed2006

A method for acoustic parameter measurement of viscoelastic material.

A method for acoustic parameters measurement of viscoelastic material, using the directivity pattern of scattering field of spherical sample made by that material, had been presented. Aluminum spheres had been used for verification of the accuracy of this method, and the measurement results of a kind of rubber had been given. It shows that this method can be used to measure parameters of viscoelastic material in sufficient wide frequency range.

Journal Article↗

PubMed2006

Theoretical analysis on retention behavior of pigments in reversed-phase high-performance liquid chromatographic (HPLC).

Quantitative structure-retention relationship (QSRR) models have been used successfully to predict and explain retention behavior of pigments in reversed-phase high-performance liquid chromatography (HPLC). The semi-empirical quantum chemical method (PM3) in Gaussian98 was employed to calculate a set of molecular descriptors of pigments. Using multiple linear regression (MLR), we obtained empirical functions with high correlation coefficient between retention times and quantum-chemical descriptors. This analysis indicated that the proposed QSRR models were satisfactory.

Chromatography, High Pressure Liquid↗

PubMed2006

Method of x-ray anomalous diffraction for lipid structures.

The structures of the unit cells of lipid phases that exhibit long-range crystalline order but short-range liquid-like disorder are of biological interests. In particular, the recently discovered rhombohedral phase has a unit cell containing either the structure of a membrane fusion intermediate state or that of a peptide-induced transmembrane pore, depending on the lipid composition and participating peptides. Diffraction from such systems generally presents a difficult phase problem. The existing methods of phase determination all have their limitations. Therefore it is of general interest to develop a new phasing method. The method of multi-wavelength anomalous dispersion is routinely used in protein crystallography, but the same method is difficult for lipid systems for the practical reason that the commonly used lipid samples for diffraction do not have a well-defined thickness. Here we describe a practical approach to use the multi-wavelength anomalous dispersion method for lipid structures. The procedure is demonstrated with the lamellar phase of a brominated lipid. The method is general to all phases as long as anomalous diffraction is applicable.

Bromine↗