Biomedical subjects

Yue Li

Publications and source records attributed to Yue Li.

At least 19 recordsLinked to original sources

PubMed2026

Integrated analysis uncovers exogenous induction and molecular regulation of erinacine A accumulation in Hericium erinaceus.

Erinacine A, a cyathane-type diterpenoid mainly from Hericium erinaceus mycelia, exhibits prominent neurotrophic and neuroprotective activities, making it a promising candidate for managing neurodegenerative diseases. However, its low abundance and unclear genetic regulatory mechanisms hinder its application as a nutraceutical. This study aimed to decipher its regulatory mechanisms and enhance production. Four exogenous inducers were screened, with salicylic acid (SA) and ergosterol (ERG) significantly increasing erinacine A content by 62.21% and 146.70% at 20 days, respectively. Transcriptome and WGCNA of inducer-treated sample identified darkorange and magenta modules associated with erinacine A biosynthesis, with the eri gene cluster enriched in the darkorange module and eriG and eriF as hub genes. Forward genetic analysis via QTL mapping of the HeD127 dikaryon population revealed significant phenotypic variation in erinacine A content (0.341-13.085 mg/g) and identified two loci (erA-1 and erA-2) explaining 18.63% of phenotypic variation. Integrating these forward and reverse genetic analyses revealed that salicylic acid and ergosterol synergistically regulate core carbon metabolic pathways to augment acetyl-CoA supply for the mevalonate pathway, suppressed competitive metabolism, enhanced diterpene skeleton construction and structural modification. These results deepen our understanding of the genetic and molecular basis governing accumulation of erinacine A, and facilitate its application in neuroprotective pharmaceuticals.

Diterpenes↗

PubMed2026

Haplotype-resolved 3D genome maps reveal RNAPII-mediated allelic regulation in hybrid rice.

To understand how the two parental genomes coordinate transcription in hybrids, chromatin architecture must be resolved at the haplotype level. Here, using phased Bridge-Linker Hi-C, we reconstructed a haplotype-resolved three-dimensional (3D) genome of the elite hybrid rice (Oryza sativa) line Shanyou 63 (SY63). We identified extensive allele-specific chromatin conformations. Furthermore, we generated allele-resolved RNAPII ChIA-PET maps and phased transcriptomes to explore how chromatin interactions contribute to allelic regulation. Although maternal and paternal homologs share broadly similar chromatin features, we detected widespread haplotype-biased RNAPII binding and chromatin looping at high resolution. These allele-specific RNAPII-mediated contacts were significantly associated with biased expression. Stronger RNAPII binding on one haplotype promoted the formation of long-range regulatory loops with distal genes, thereby contributing to allele-biased transcription at a subset of loci, even when promoter-proximal RNAPII occupancy was comparable between alleles. These results demonstrate that subtle differences in RNAPII engagement and 3D regulatory wiring between parental haplotypes can reshape transcriptional output in hybrids, providing new insights into the mechanisms underlying the allelic regulation of gene expression.

Allele-specific chromatin interactions↗

PubMed2026

DNA-aware evaluation and debiasing of sequence-to-function models.

MOTIVATION: Genome sequence-to-function (S2F) models are widely used to interpret base-resolution functional genomics assays. Most S2F models are trained and evaluated against observed counts and profile-shapes using statistical objectives and fidelity metrics. These choices are well motivated, but they are DNA-independent. At the same time, experimental measurements arise from DNA-dependent assays with distinct characteristics. This mismatch motivates a complementary DNA-aware evaluation of S2F-predicted and experimental functional genomic tracks. RESULTS: We study DNA-dependency of experimental and S2F-predicted tracks using track-conditional genome language models (cgLMs). cgLMs predict masked nucleotides from a conditioning track under controlled DNA visibility. Across ATAC-seq and TF ChIP-seq peaks from GM12878 and K562, cgLM-probing reveals a consistent masked DNA-decodability gap between many experimental and S2F-predicted tracks. In particular, single-task (e.g. BPNet) and multi-task (e.g. AlphaGenome) S2F-predicted tracks enabled cgLMs to recover masked nucleotides with significantly higher accuracy and confidence than matched experimental tracks. Analyses of nonpeak and dinucleotide-shuffled sequences show that this gap is not confined to peaks and is not captured by standard DNA-agnostic profile-shape fidelity metrics alone. ChromBPNet Tn5-denoised predictions were an exception and behaved closer to the experimental regime, suggesting that staged training may reduce the gap. We then convert this diagnostic into a critic-derived objective, DNA-dependency matching (DDM), using a frozen multi-headed cgLM critic. We introduce Critic-Guided Profile-Shape Editing (CGPSE), a preliminary post hoc debiasing framework for frozen S2F models. In GM12878 ATAC-seq, CGPSE partially reduces the masked DNA-decodability gap for AlphaGenome and BPNet predictions, while exposing a tradeoff with profile-shape fidelity. AVAILABILITY AND IMPLEMENTATION: https://github.com/li-lab-mcgill/dna-aware-s2f-eval.

DNA↗

PubMed2025

Sparse polygenic risk score inference with the spike-and-slab LASSO.

MOTIVATION: Large-scale biobanks, with rich phenotypic and genomic data across hundreds of thousands of samples, provide ample opportunities to elucidate the genetics of complex traits and diseases. Consequently, there is growing demand for robust and scalable methods for disease risk prediction from genotype data. Inference in this setting is challenging due to the high-dimensionality of genomic data, especially when coupled with smaller sample sizes. Popular Polygenic Risk Score (PRS) inference methods address this challenge by adopting sparse Bayesian priors or penalized regression techniques, such as the Least Absolute Shrinkage and Selection Operator (LASSO). However, the former class of methods are not as scalable and do not produce exact sparsity, while the latter tends to over-shrink large coefficients. RESULTS: In this study, we present SSLPRS, a novel PRS method based on the Spike-and-Slab LASSO (SSL) prior, which offers a theoretical bridge between the two frameworks. We extend previous work to derive a coordinate-ascent inference algorithm that operates on GWAS summary statistics, which is orders-of-magnitude more efficient than corresponding individual-level-based implementations. To illustrate the statistical properties of the proposed model, we conducted experiments involving nine simulation configurations and nine quantitative phenotypes from the UK Biobank. Our results demonstrate that SSLPRS is competitive with state-of-the-art methods in terms of prediction accuracy and exhibits superior variable selection performance, especially in sparse genetic architectures. In simulations, this translates to upwards of 50% improvement in positive predictive value. In analysis of real phenotypes, we show that selected variants are highly enriched for meaningful genomic annotations and have better replication rates in larger meta-analyses. AVAILABILITY AND IMPLEMENTATION: SSLPRS is available in the open-source package https://github.com/li-lab-mcgill/penprs.

Multifactorial Inheritance↗

PubMed2025

Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and Tumor-Immune Microenvironment.

Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial-temporal diversity and influence on tumor evolution and the immune microenvironment remain largely unclear. We apply computational methods to analyze ecDNA from whole-genome sequencing data of 595 urothelial carcinoma (UC) patients. We demonstrate that ecDNA drives clonal evolution through structural rearrangements during malignant transformation and recurrence of UC. This supports a model wherein tumors evolve via the selective expansion of ecDNA-bearing cells. Through multi-regional sampling of tumors, we demonstrate that ecDNA contributes to the evolution of multifocality and increased intratumoral heterogeneity. EcDNA is present in 36% of UC tumors and correlates with an immunosuppressive phenotype and poor prognosis. Single-cell RNA sequencing analyses reveal that ecDNA+ malignant cells exhibit diminished expression of major histocompatibility complex class I molecules, enabling them to evade T-cell immunity. Finally, we show that sequencing of urinary sediment-derived DNA has excellent specificity in detecting ecDNA.

Journal Article↗

PubMed2024

SLC40A1-related hemochromatosis associated with a p.Y333H mutation in mainland China: a pedigree report and literature review.

BACKGROUND: Haemochromatosis is a genetic disease characterized by the excessive deposition of iron in various tissues and organs, eventually results in organ damage including cirrhosis, diabetes, cardiomyopathy, etc. SLC40A1-related haemochromatosis is associated with gain-of-function mutations in the SLC40A1 gene, which encodes ferroportin. While sporadic reports of this condition exist in mainland China, the understanding of the phenotype and genetic pattern associated with the SLC40A1 p.Y333H mutation remains incomplete. CASE PRESENTATION: We report a pedigree with heterozygous p.Y333H mutation in Chinese Han population. The proband is a 64-year-old man complaining of persistent abnormality of liver enzyme levels for 1 year, with a history of knee joint pain, diabetes and skin pigmentation. He displayed markedly elevated serum ferritin level and transferrin saturation. Magnetic resonance imaging showed iron deposition in the liver, spleen, and pancreas, along with cirrhosis and splenomegaly. Whole exome sequencing identified a heterozygous allelic variant c.997T > C (p.Y333H). Genetic screening of family members identified four first-degree relatives and three second-degree relatives having the same mutation. Additional cases with this mutation from two published studies were included. Among the probands and screened relatives, all eight males aged over 30 y had ferritin level > 1000 µg/L, transferrin saturation > 90%. Four patients with organ damage in the present study received therapeutic phlebotomy, alleviating clinical symptoms and improving in transferrin saturation and serum ferritin. CONCLUSIONS: This study reports the largest pedigree with heterozygous SLC40A1 p.Y333H mutation in the Chinese population to date. In Chinese families, males over 30 years old with hemochromatosis due to SLC40A1 p.Y333H mutation exhibit severe iron overload phenotypes.

Humans↗

PubMed2024

Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique.

The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.

Deep Learning↗

PubMed2007

Atmospheric pressure molecular imaging by infrared MALDI mass spectrometry.

An atmospheric pressure (AP) MALDI imaging interface was developed for an orthogonal acceleration time-of-flight mass spectrometer and utilized to analyze peptides, carbohydrates, and other small biomolecules using infrared laser excitation. In molecular imaging experiments, the spatial distribution of mock peptide patterns was recovered with a detection limit of approximately 1 fmol/pixel from a variety of MALDI matrixes. With the use of oversampling for the image acquisition, a spatial resolution of 40 microm, 5 times smaller than the laser spot size, was achieved. This approach, however, required that the analyte was largely removed at the point of analysis before the next point was interrogated. Native water in plant tissue was demonstrated to be an efficient natural matrix for AP infrared laser desorption ionization. In soft fruit tissues from bananas, grapes, and strawberries, potassiated ions of the most abundant metabolites, small carbohydrates, and their clusters produced the strongest peaks in the spectra. Molecular imaging of a strawberry skin sample revealed the distribution of the sucrose, glucose/fructose, and citric acid species around the embedded seeds. Infrared AP MALDI mass spectrometric imaging without the addition of an artificial matrix enables the in vivo investigation of small biomolecules and biological processes (e.g., metabolomics) in their natural environment.

Journal Article↗

PubMed2007

Implementation of the near-field signal redundancy phase-aberration correction algorithm on two-dimensional arrays.

Near-field signal-redundancy (NFSR) algorithms for phase-aberration correction have been proposed and experimentally tested for linear and phased one-dimensional arrays. In this paper the performance of an all-row-plus-two-column, two-dimensional algorithm has been analyzed and tested with simulated data sets. This algorithm applies the NFSR algorithm for one-dimensional arrays to all the rows as well as the first and last columns of the array. The results from the two column measurements are used to derive a linear term for each row measurement result. These linear terms then are incorporated into the row results to obtain a two-dimensional phase aberration profile. The ambiguity phase aberration profile, which is the difference between the true and the derived phase aberration profiles, of this algorithm is not linear. Two methods, a trial-and-error method and a diagonal-measurement method, are proposed to linearize the ambiguity profile. The performance of these algorithms is analyzed and tested with simulated data sets.

Algorithms↗

PubMed2006

Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residues.

Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) in the folate biosynthetic pathway. There are four conserved active site residues at the active site, E22, Y54, E74, and K100 in Staphylococcus aureus DHNA (SaDHNA), corresponding to E21, Y53, E73, and K98, respectively, in Escherichia coli DHNA (EcDHNA). The functional roles of the conserved glutamate and lysine residues have been investigated by site-directed mutagenesis in this work. E22 and E74 of SaDHNA and E21, E73, and K98 of EcDHNA were replaced with alanine. K100 of SaDHNA was replaced with alanine and glutamine. The mutant proteins were characterized by equilibrium binding, stopped-flow binding, and steady-state kinetic analyses. For SaDHNA, none of the mutations except E74A caused dramatic changes in the affinities of the enzyme for the substrate or product analogues or the rate constants. The Kd values for SaE74A were estimated to be >3000 microM, suggesting that the Kd values of the mutant are at least 100 times those of the wild-type enzyme. For EcDHNA, the E73A mutation increased the Kd values for the substrate or product analogues neopterin (MP), monapterin (NP), and 6-hydroxypterin (HPO) by factors of 340, 160, and 5600, respectively, relative to those of the wild-type enzyme. The K98A mutation increased the Kd values for NP, MP, and HPO by factors of 14, 3.6, and 230, respectively. The E21A mutation increased the Kd values for NP and HPO by factors of 2.2 and 42, respectively, but decreased the Kd value for MP by a factor of 3.3. The E22 (E21) and K100 (K98) mutations decreased the kcat values by factors of 1.3-2 x 10(4). The E74 (E73) mutation decreased in the kcat values by factors of approximately 10. The results suggested that E74 of SaDHNA and E73 of EcDHNA are important for substrate binding, but their roles in catalysis are minor. In contrast, E22 and K100 of SaDHNA are important for catalysis, but their roles in substrate binding are minor. On the other hand, E21 and K98 of EcDHNA are important for both substrate binding and catalysis.

Aldehyde-Lyases↗

PubMed2006

Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY.

A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids.

Amides↗

PubMed2006

Effects of Cilazapril on atrial electrical, structural and functional remodeling in atrial fibrillation dogs.

BACKGROUND AND PURPOSE: The effects of angiotensin-converting enzyme inhibitor on long-term atrial electrophysiologic and structural remodeling are still unclear. The purpose of this study is to investigate the effects of Cilazapril on atrial electrical, structural, and functional remodeling in atrial fibrillation (AF) dogs induced by chronic rapid atrial pacing. METHODS: Twenty dogs were randomly divided into sham-operated group (n = 6), control group (n = 7), and Cilazapril group (n = 7). One thin silicon plaque containing 4 pairs of electrodes was sutured to each atrium. A pacemaker was implanted in a subcutaneous pocket and attached to a screw-in epicardial lead in the right atrial appendage. The dogs in control group and Cilazapril group were paced at 400 beats per minute for 6 weeks. The dogs in Cilazapril group received Cilazapril (0.5 mg x kg(-1) x d(-1)) 1 week before rapid atrial pacing until pacing stop. Before and after 6-week rapid atrial pacing, atrial effective refractory period (AERP) at 8 sites, AERP dispersion, intraatrium conduction time, inducibility, and duration of AF were measured. Transthoracic and transesophageal echocardiographic examinations included left atrium (LA) maximal volume, LA minimal volume, LA ejection fraction, left atrial appendage (LAA) maximal volume, LAA minimal volume, LAA ejection fraction, LAA maximal forward flow velocity, and LAA minimal backward flow velocity were performed. Atrial collagen volume fraction was analyzed by Masson staining. RESULTS: After 6-week rapid atrial pacing, although there was no significant difference in AERP shortening and AERP rate adaptation reduction between the control group and the Cilazapril group, the inducibility and duration of AF were found to be dramatically lower in the Cilazapril group than those in the control group (AF inducibility, 65.7% vs 95.7%, P < .05; AF duration, 531.5 +/- 301.2 vs 1432.2 +/- 526.5 s, P < .01). The post-tachycardia intraatrium conduction times after 6 weeks with Cilazapril were significantly shorter than those in the control group. Cliazapril could partially prevent AERP dispersion increase induced by chronic rapid atrial pacing. Compared with the control group, the LA and LAA volumes were significantly smaller; LA ejection fraction, LAA ejection fraction, LAA maximal forward flow velocity, and LAA minimal backward flow velocity were dramatically higher in the Cilazapril group. The Cilazapril group had a significantly lower percentage of interstitial fibrosis than the control group. CONCLUSIONS: Cilazapril can suppress structural and functional remodeling and prevent the induction and promotion of AF in chronic rapid atrial pacing dogs.

Angiotensin-Converting Enzyme Inhibitors↗

PubMed2006

Antigen-specific tolerance induced by IL-10 gene modified immature dendritic cells in experimental autoimmune myocarditis in rats.

BACKGROUND: Experimental autoimmune myocarditis (EAM) in rats is a T-cell-mediated disorder. The initiation and maintenance of autoimmune responses in EAM depend on the maturation state of dendritic cells. IL-10 is a pleiotrophic immunomodulatory cytokine that functions at different levels of the immune response, so it has emerged as a promising therapeutic factor for the treatment of autoimmune/inflammatory diseases. This study was designed to test the hypothesis that IL-10 gene modified bone marrow-derived immature dendritic cells (iDCs) ameliorate EAM and to explore the underlying mechanisms. METHODS: EAM was induced using the methods of cardiac myosin immunization on day 0 and day 7. Immature and mature bone marrow-derived dendritic cells (BMDCs) were generated without or with the stimulation by lipopolysaccharide (LPS) and the phenotype was analyzed by flow cytometry. Some of the iDCs were transfected by pcDNA3-IL-10 plasmid. 2 x 10(6)/per rat mature DC (mDC), immature DC (iDC), pcDNA3 transfected iDC, pcDNA3-IL-10 transfected iDC or phosphate buffered saline (PBS) were injected intravenously for treatment 5 days after the first immunization. On day 21, HE staining was performed to detect the myocardial inflammation and T lymphocyte proliferation assay was used to determine the effects of IL-10 gene transfected iDC on autoreactive T cell proliferation. Expression of IkappaB, the inhibitor of NF-kappaB pathway, was determined by Western blot. RESULTS: BMDCs generated in a medium supplemented with granulocyte-macrophage-colony-stimulating factor (GM-CSF) were relatively immature, as determined by flow cytometry. However, stimulation with LPS induced these cells to become mature (m) DCs with higher levels of surface major histocompatibility complex (MHC)-II and costimulatory molecules. Intravenous administration of iDCs, especially pcDNA3-IL-10 transfected iDC, ameliorated the histopathological severity of the myosin induced-EAM, and the effect was lost after the DCs underwent maturation induced by in vitro exposure to LPS. IL-10 gene modified iDC inhibited the antigen specific T cell responses towards cardiac myosin. IkappaB protein was up-regulated significantly in the IL-10 gene modified iDC group. CONCLUSIONS: IL-10 gene modified iDC induced antigen-specific tolerance in EAM. The underlying mechanisms may be related to costimulatory molecules down-regulation and NF-kappaB pathway inhibition.

Animals↗

PubMed2006

Screening high-fluoride and high-arsenic drinking waters and surveying endemic fluorosis and arsenism in Shaanxi province in western China.

The objectives of this study were to screen high-fluoride and high-arsenic drinking waters, to evaluate the effectiveness of fluoride-reducing projects and to assess the present condition of endemic fluorosis and arsenism in Shaanxi province in western China. For screening high-fluoride drinking waters, five water samples were collected from each selected village where dental fluorosis patients were detected in 8-12 year-old children. For evaluating the effectiveness of fluoride-reducing projects, four water samples were collected from each project at end-user level. Fluoride concentrations in water samples were measured by fluoride-selective electrode method or spectrophotometry. Dental fluorosis in children aging 8-12 years was examined according to Horowitz's Tooth Surface Index of Fluorosis. Skeletal fluorosis in adults was detected clinically and radiologically according to Chinese Criteria of Clinical Diagnosis of Skeletal Fluorosis. For screening high-arsenic waters, 20 water samples were collected from each village which was selected from areas characterized by the geographic features to induce high-arsenic underground water, i.e., alluvial plains, ore mining or smelting areas, geothermal artesians, and thermal springs. Arsenic concentrations in water samples were determined by spectrophotometry or arsine generation atomic fluorospectrophotometry. Arsenism in adults aging 40-89 years was examined in villages with arsenic concentrations in drinking water above 0.05 mg/l according to Chinese Criteria for Classification of Endemic Arsenism Areas and Clinical Diagnoses of Endemic Arsenism. The results showed that the fluoride level of 7144 water samples was 1.17 +/- 0.93 mg/l. There were 3396 (47.6%) high-fluoride waters (fluoride level was above 1.0 mg/l) distributing in 786 (45.1%) villages, where about 0.8 million (50.0%) people inhabited. Additionally, the 1315 fluoride-reducing projects were studied. The fluoride level of the projects was 2.79 +/- 1.09 and 0.98 +/- 0.47 mg/l before and after building the projects, which remained at relatively lower level (1.03 +/- 0.47 mg/l). But there were still 58.0% of the projects providing drinking waters with fluoride concentrations beyond 1.0mg/l. The rates of dental fluorosis and skeletal fluorosis were 38.2% and 11.8%, respectively. The arsenic level of 1732 water samples was 0.010 +/- 0.082 mg/l. There were 174 (14.9%) high-arsenic waters (arsenic level was above 0.010 mg/l) being detected, distributing in 41 (38.7%) villages. The arsenic level in 53 (4.5%) water samples was beyond 0.025 mg/l. There were 3 villages with arsenic level in drinking water beyond Chinese National Permissible Limits (0.050 mg/l), and the prevalence rate of arsenism reached 37.0% in these three villages, 3.7%, 22.2%, and 11.1% of subjects suffering from mild, moderate, and severe arsenism, respectively. Conclusively, the wide distribution of high-fluoride drinking waters contributes to the prevalence of dental and skeletal fluorosis in Shaanxi province and the quality of fluoride-reducing projects should be further improved. Ore mining and smelting induces high-arsenic drinking waters, resulting in arsenism prevalence in Shang-luo city. Proper measures should be taken to deal with water pollution in the ore mining and smelting areas in order to solve the high-arsenic water problem in Shaanxi province.

Adult↗

PubMed2006

IL-10 gene modified dendritic cells induced antigen-specific tolerance in experimental autoimmune myocarditis.

Experimental autoimmune myocarditis (EAM) in rats is a T-cell-mediated disorder, and the involvement of Th1/Th2 unbalance has been demonstrated. The induction of antigen-specific tolerance is critical for the treatment of EAM and maintenance of immune tolerance. IL-10 is a pleiotrophic immunomodulatory cytokine that functions at different levels of the immune response, so it has emerged as a promising therapeutic factor for the treatment of autoimmune/inflammatory diseases. This study was designed to explore the effects of IL-10 gene modified bone-marrow-derived immature dendritic cells (iDCs) on the in vitro and in vivo immune response to cardiac myosin in EAM. EAM was induced using the classic methods of cardiac myosin immunization on day 0 and day 7. 2 x 10(6)/per rat mature DC (mDC), immature DC (iDC), pcDNA3 transfected iDC, pcDNA3-IL-10 transfected iDC or PBS were injected intravenously for treatment 5 days after the first immunization. On day 21, transthoracic echocardiogram and HE staining were performed to detect the cardiac function and myocardial inflammation. Th1/Th2 cytokines were detected by ELISA and MHC-II molecules, costimulatory molecules were identified by flow cytometry. In vitro T lymphocyte proliferation assay and adoptive transfer of DCs were performed to determine the antigen-specific tolerance induced by IL-10 gene modified iDCs. IL-10 gene modified iDC-treated EAM rats showed improved cardiac function and reduced infiltration of inflammatory cell into myocardium. Serum cytokines data indicated lower Th1 while higher Th2-type responses were induced in the pcDNA3-IL-10-iDC-treated group, suggesting a Th2 polarization. Moreover, IL-10 gene modified iDCs down-regulated MHC-II and costimulatory molecules on the surface of splenocytes and inhibited the antigen-specific immunological responses towards cardiac myosin. Adoptive transfer of IL-10 producing DCs prevented EAM induction. IL-10 gene modified iDCs ameliorates EAM histopathologically and functionally. The underlying mechanisms may be related to the IL-10 induced Th2 polarization and down-regulation of MHC-II molecules and costimulatory molecules expression.

Adoptive Transfer↗

PubMed2006

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue.

Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs, because the pathway is essential in microorganisms, plants, and parasites but absent from mammals. SK catalyzes the reaction of phosphoryl transfer from ATP to shikimic acid (SA). Since 2002, a total of 11 SK structures have been reported, but none contains either the two substrate (SA and ATP) or the two product (SA-phosphate and ADP) molecules. Here, we present three crystal structures of SK from Mycobacterium tuberculosis (MtSK), including apo-MtSK, a binary complex MtSK x SA, and the ternary complex of MtSK with SA and an ATP analogue, AMPPCP. The structures of apo-MtSK and MtSK x AMPPCP x SA make it possible to elucidate the conformational changes of MtSK upon the binding of both substrates; the structure of MtSK x AMPPCP x SA reveals interactions between the protein and gamma-phosphate which indicate dynamic roles of catalytic residues Lys15 and Arg117.

Adenosine Triphosphate↗

PubMed2006

Transferable ordered ni hollow sphere arrays induced by electrodeposition on colloidal monolayer.

We report an electrochemical synthesis of two-dimensionally ordered porous Ni arrays based on polystyrene sphere (PS) colloidal monolayer. The morphology can be controlled from bowl-like to hollow sphere-like structure by changing deposition time under a constant current. Importantly, such ordered Ni arrays on a conducting substrate can be transferred integrally to any other desired substrates, especially onto an insulting substrate or curved surface. The magnetic measurements of the two-dimensional hollow sphere array show the coercivity values of 104 Oe for the applied field parallel to the film, and 87 Oe for the applied field perpendicular to the film, which is larger than those of bulk Ni and hollow Ni submicrometer-sized spheres. The formation of hollow sphere arrays is attributed to preferential nucleation on the interstitial sites between PS in the colloidal monolayer and substrate, and growth along PSs' surface. The transferability of the arrays originates from partial contact between the Ni hollow spheres and substrate. Such novel Ni ordered nanostructured arrays with transferability and high magnetic properties should be useful in applications such as data storage, catalysis, and magnetics.

Journal Article↗

PubMed2006

Dynamics study of the reaction OH- + C2H2-->C2H- + H2O with crossed beams and density-functional theory calculations.

The proton transfer reaction between OH- and C2H2, the sole reactive process observed over the collision energy range from 0.37 to 1.40 eV, has been studied using the crossed beam technique and density-functional theory (DFT) calculations. The center of mass flux distributions of the product C2H- ions at three different energies are highly asymmetric, characteristic of a direct process occurring on a time scale much less than a rotational period of any transient intermediate. The maxima in the flux distributions correspond to product velocities and directions close to those of the precursor acetylene reactants. The reaction quantitatively transforms the entire exothermicity into internal excitation of the products, consistent with an energy release motif in which the proton is transferred early, in a configuration in which the forming bond is extended. This picture is supported by DFT calculations showing that the first electrostatically bound intermediate on the reaction pathway is the productlike C2H- H2O species. Most of the incremental translational energy in the two higher collision energy experiments appears in product translational energy, and provides an example of induced repulsive energy release characteristic of the heavy+light-heavy mass combination.

Journal Article↗