Biomedical subjects

Yiming Yang

Publications and source records attributed to Yiming Yang.

17 recordsLinked to original sources

PubMed2026

Tandem Duplication-Driven Neofunctionalization of UDP-Glycosyltransferases Shapes the Diversification of Triterpenoid Saponins in the Cucurbitaceae.

Tandem duplication of tailoring enzymes allows evolutionary innovation that diversifies plant specialized metabolism. Here, we present an interesting example of how tandem duplicated UDP-glycosyltransferases undergo neofunctionalization and shape the chemical diversity of triterpenoid saponins in the Cucurbitaceae family. A chromosome-level genome of Siraitia grosvenorii was assembled and aligned with multiple cucurbit genomes, revealing a specific UGT73AM tandem duplication responsible for regio-selective glycosylation (e.g. the rare 1,4-linked disaccharide) of diverse saponins such as mogrosides, ginsenosides, and momordicines. Comparative genomics depicted the evolutionary trajectory of a universal saponin-biosynthesizing UGT73 tandem arrays syntenously preserved across core eudicots, where lineage-specific UGT copies contribute to distinct metabolic phenotypes. A crystal structure of SgUGT73AM30 (mogrol 25-O-glycosyltransferase) in complex with UDP and mogrol was obtained to elucidate the molecular basis of the regio-specific decoration on vicinal diol of the substrates. Altogether, these findings provide insights into tandem duplication-driven diversification of glycosyltransferases and lay the foundation for engineered glycosylation of valuable triterpenoid saponins.

Saponins↗

PubMed2006

Characterization and quantification of eight water-soluble constituents in tubers of Pinellia ternata and in tea granules from the Chinese multiherb remedy Xiaochaihu-tang.

In traditional Chinese medicine, multiple herbs are usually used in combination to generate the joint actions of a multiherb remedy. The recent development of LC-hyphenated techniques enables efficient and rapid profiling of the chemical constituent in extracts from multiherb remedies. Xiaochaihu-tang is a seven-herb remedy that has attracted a great deal of attention for reported ability to treat liver dysfunction. Dried tubers of Pinellia ternata (banxia in Chinese) is one of the ingredients, but its chemical contribution to Xiaochaihu-tang remains poorly understood. In the study presented here, LC-UV-MS, LC-MS-MS, and LC-NMR were used in a complementary manner to determine the nature and content of eight water-soluble constituents of banxia and their presence in various tea granules from Xiaochaihu-tang. Among the eight chemicals identified in banxia, cytidine, adenosine, tryptophan, uridine, and adenine are reported for the first time, while tyrosine, guanosine, and phenylalanine were previously described. These chemicals are also present in all of the samples of Xiaochaihu-tang granules, and the amounts of the chemicals ingested due to a daily dose of the multiherb remedies range from 0.008 to 6.3mg.

Adenine↗

PubMed2005

Analysis of recursive gene selection approaches from microarray data.

MOTIVATION: Finding a small subset of most predictive genes from microarray for disease prediction is a challenging problem. Support vector machines (SVMs) have been found to be successful with a recursive procedure in selecting important genes for cancer prediction. However, it is not well understood how much of the success depends on the choice of the specific classifier and how much on the recursive procedure. We answer this question by examining multiple classifers [SVM, ridge regression (RR) and Rocchio] with feature selection in recursive and non-recursive settings on three DNA microarray datasets (ALL-AML Leukemia data, Breast Cancer data and GCM data). RESULTS: We found recursive RR most effective. On the AML-ALL dataset, it achieved zero error rate on the test set using only three genes (selected from over 7000), which is more encouraging than the best published result (zero error rate using 8 genes by recursive SVM). On the Breast Cancer dataset and the two largest categories of the GCM dataset, the results achieved by recursive RR are also very encouraging. A further analysis of the experimental results shows that different classifiers penalize redundant features to different extent and this property plays an important role in the recursive feature selection process. RR classifier tends to penalize redundant features to a much larger extent than the SVM does. This may be the reason why recursive RR has a better performance in selecting genes.

Algorithms↗

PubMed2005

A new beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Helicobacter pylori: Molecular cloning, enzymatic characterization, and structural modeling.

Helicobacter pylori is a gram-negative pathogenic bacterium that causes peptic ulcer disease and gastric cancer, and studies of the related potent enzymes associated with this bacterium are urgent for the discovery of novel drug targets. In bacteria, beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase (FabZ) is a potent enzyme in fatty acid biosynthesis and catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP. In this study, the cloning and enzymatic characterization of FabZ from H. pylori strain SS1 (HpFabZ) were reported, and the gene sequence of HpfabZ was deposited in the GenBank database. Enzyme dynamic analysis showed that HpFabZ had a K(m) of 82.6+/-4.3 microM toward its substrate analog crotonoyl-CoA. Dynamic light scattering and native-PAGE investigations suggested that HpFabZ exists as hexamer in native state. Enzymatic characterization and thermal-induced unfolding analysis based on circular dichroism spectral measurements indicated that HpFabZ is very stable against high temperature (90 degrees C). Such a high stability of HpFabZ was well elucidated by the strong H-bonds and hydrophobic interactions among the HpFabZ hexamer as investigated in the modeled HpFabZ hexamer structure. Our current study is hoped to provide useful information in better understanding the FabZ of H. pylori strain and further supply possible hints in the discovery of anti-bacterial compounds using HpFabZ as target.

Amino Acid Sequence↗

PubMed2005

Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro.

The 3C-like proteinase (3CLpro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for anti-SARS-CoV drugs due to its crucial role in the viral life cycle. In this study, a database containing structural information of more than 8,000 existing drugs was virtually screened by a docking approach to identify potential binding molecules of SARS-CoV 3CLpro. As a target for screening, both a homology model and the crystallographic structure of the binding pocket of the enzyme were used. Cinanserin (SQ 10,643), a well-characterized serotonin antagonist that has undergone preliminary clinical testing in humans in the 1960s, showed a high score in the screening and was chosen for further experimental evaluation. Binding of both cinanserin and its hydrochloride to bacterially expressed 3CLpro of SARS-CoV and the related human coronavirus 229E (HCoV-229E) was demonstrated by surface plasmon resonance technology. The catalytic activity of both enzymes was inhibited with 50% inhibitory concentration (IC50) values of 5 microM, as tested with a fluorogenic substrate. The antiviral activity of cinanserin was further evaluated in tissue culture assays, namely, a replicon system based on HCoV-229E and quantitative test assays with infectious SARS-CoV and HCoV-229E. All assays revealed a strong inhibition of coronavirus replication at nontoxic drug concentrations. The level of virus RNA and infectious particles was reduced by up to 4 log units, with IC50 values ranging from 19 to 34 microM. These findings demonstrate that the old drug cinanserin is an inhibitor of SARS-CoV replication, acting most likely via inhibition of the 3CL proteinase.

Animals↗

PubMed2004

In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS.

The major biochemical and thermodynamic features of nucelocapsid protein of SARS coronavirus (SARS_NP) were characterized by use of non-denatured gel electrophoresis, size-exclusion chromatographic and surface plasmon resonance (SPR) techniques. The results showed that SARS_NP existed in vitro as oligomer, more probably dimer, as the basic functional unit. This protein shows its maximum conformational stability near pH 9.0, and it seems that its oligomer dissociation and protein unfolding occur simultaneously. Thermal-induced unfolding for SARS_NP was totally irreversible. Both the thermal and chemical denaturant-induced denaturation analyses showed that oligomeric SARS_NP unfolds and refolds through a two-state model, and the electrostatic interactions among the charge groups of SARS_NP made a significant contribution to its conformational stability.

Chromatography, Gel↗

PubMed2004

Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A.

Severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for SARS infection. Nucleocapsid protein (NP) of SARS-CoV (SARS_NP) functions in enveloping the entire genomic RNA and interacts with viron structural proteins, thus playing important roles in the process of virus particle assembly and release. Protein-protein interaction analysis using bioinformatics tools indicated that SARS_NP may bind to human cyclophilin A (hCypA), and surface plasmon resonance (SPR) technology revealed this binding with the equilibrium dissociation constant ranging from 6 to 160nM. The probable binding sites of these two proteins were detected by modeling the three-dimensional structure of the SARS_NP-hCypA complex, from which the important interaction residue pairs between the proteins were deduced. Mutagenesis experiments were carried out for validating the binding model, whose correctness was assessed by the observed effects on the binding affinities between the proteins. The reliability of the binding sites derived by the molecular modeling was confirmed by the fact that the computationally predicted values of the relative free energies of the binding for SARS_NP (or hCypA) mutants to the wild-type hCypA (or SARS_NP) are in good agreement with the data determined by SPR. Such presently observed SARS_NP-hCypA interaction model might provide a new hint for facilitating the understanding of another possible SARS-CoV infection pathway against human cell.

Amino Acid Sequence↗

PubMed2004

Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori.

Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K(cat) of 3.4s(-1), K(m) of 1.7 mM, and K(cat) / K(m) of 2000M(-1)s(-1). HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 degrees C. The enzyme activity of Co(2+)-containing HpPDF is apparently higher than that of Zn(2+)-containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori.

Amidohydrolases↗

PubMed2004

[Community structure and seasonal change of soil micro-arthropodes in the Lower Reaches of Liaohe River Plain under different land utilization].

The data on the soil micro-arthropodes under four land utilization types (fallow, forest, upland field and paddy) in the Lower Reaches of Liaohe River Plain were collected in a period from October 2000 to October 2001. Using the community parameters of population density, group richness, diversity index and evenness, the community structure and its seasonal changes were described. There were 12 groups of soil micro-arthropodes in this region, and of the groups, Collembola and Acarina were dominant, and Diptera, Coleoptera and Hymenoptera were often seen in fallow, forest and upland field, while Collembola, Acarina and Diptera were dominant in paddy. Both land utilization and seasonal change influenced the population density, group richness and diversity index of soil micro-arthropodes. The vertical distribution in both density and group number of arthropods in soil was in the order of surface > middle > bottom.

Agriculture↗

PubMed2004

Recovering genetic regulatory networks from micro-array data and location analysis data.

Learning large network (with hundreds of variables) is gaining interest of many researchers with the emergence of high-throughput biological data sources such as micro-array data. In this paper, we investigated the two popular large scale network structure learning algorithms, sparse candidate hill climbing (SCHC) and Grow-Shrinkage(GS) algorithm. The experiments show that in fact both of them have serious effectiveness problems when the number of variables(genes) is large compared to the number of instances(experimental conditions), which is a common case in micro-array data. We further propose a new large scale structure learning algorithm based on Lasso regression. Theoretical analysis in [10] suggested that the L1-norm in lasso regression could make our algorithm especially suitable in the cases that the number of variables and instances is unbalance. Our algorithm achieves much better results than SCHC and GS on the synthetic data. We also show the effectiveness of our algorithm by learning genetic regulatory network modules from a real micro-array data (with more than 6000 genes), combined with the genome-wide location analysis data. The learned results are consistent well with biological knowledge.

Algorithms↗

PubMed2003

Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus.

Severe acute respiratory syndrome (SARS) is an acute respiratory illness, which has broken out in China. It has been known that SARS coronavirus (SARS_CoV) is a novel human coronavirus and is responsible for SARS infection. Belonging to one of the major proteins associated with SARS_CoV, SARS 3C-like protease (SARS_3CL(pro)) functions as a cysteine protease engaging in the proteolytic cleavage of the viral precursor polyprotein to a series of functional proteins required for coronavirus replication and is considered as an appealing target for designing anti-SARS agents. To facilitate the studies regarding the functions and structures of SARS_3CL(pro), in this report the synthetic genes encoding 3CL(pro) of SARS_CoV were assembled, and the plasmid was constructed using pQE30 as vector and expressed in Escherichia coli M15 cells. The highly yielded ( approximately 15mg/L) expressed protease was purified by use of NTA-Ni(2+) affinity chromatography and FPLC system, and its sequence was determined by LC/MS with the residue coverage of 46.4%.

Amino Acid Sequence↗

PubMed2003

[The variation of Caspase3 activity in tanshinone induced NB4 cells apoptosis].

OBJECTIVE: To study the variation and role of Caspase3 activity in the process of Tanshinone (Tan II A) induced NB4 cells apoptosis. METHODS: NB4 cell apoptosis induced by Tan II A was demonstrated by cell morphology, DNA content analysis and DNA fragmentation assay. Caspase3 activity was determined by spectrofluorometry, and its inhibitory assay was performed using N-acetyl-Asp-Glu-Val-Asp-aldehyde(AC-DEVD-CHO). RESULTS: Tan II A could induce NB4 cell apoptosis accompanied with increase of caspase3 activity. The induction of NB4 cell apoptosis by use of Tan II A could be partially inhibited by AC-DEVD-CHO. CONCLUSION: The induction of NB4 cell apoptosis by Tan II A could be fulfilled by activating Caspase3.

Abietanes↗

PubMed2003

[Effect of autologous dendritic cells on chronic myeloid leukemia cells in vitro].

OBJECTIVE: To observe the effect of autologous dendritic cells (DC) on positive Philadelphia (Ph+) chromosome cells of Chronic Myeloid Leukemia (CML) in vitro. METHODS: DCs and T cells extracted from the peripheral blood mononuclear cell (PBMNC) of 4 CML patients with Ph+ chromosome in chronic phases were amplified in a special liquid culture system. The survival rates of the Ph+ chromosome cells in the bone marrow mononuclear cells (BMMNC) and the K562 cells were determined by the conventional chromosome assays, after About 3 x 10(5)/ml DC incubating with autologous T cells activated by IL-2 or DCs plus IL-2 for 6 hours. RESULTS: About 3 x 10(5)/ml DC per 2 x 10(6)/ml PBMNC were produced. The cytotoxic effect of the T cells activated by DCs plus IL-2 on the autologous Ph+ chromosome cells was significantly greater than those activated by IL-2 (P < 0.001). The clearance activity of the DC activated T cells on the autologous CML Ph+ chromosome cells was stronger than on the K562 cells (P < 0.001). CONCLUSION: The DCs-activated autologous T cells can effectively inhibit the Ph+ chromosome cells. The cytotoxic effect of the autologous T cells activated by the DCs on the Ph+ chromosome cells could be MHC-restricted.

Adult↗

PubMed2002

Receptors for chemotactic formyl peptides as pharmacological targets.

Leukocytes accumulate at sites of inflammation and immunological reaction in response to locally existing chemotactic mediators. N-formyl peptides, such as fMet-Leu-Phe (fMLF), are some of the first identified and most potent chemoattractants for phagocytic leukocytes. In addition to the bacterial peptide fMLF and the putative endogenously produced formylated peptides, a number of novel peptide agonists have recently been identified that selectively activate the high-affinity fMLF receptor FPR and/or its low-affinity variant FPRL1, both of which belong to the seven-transmembrane (STM), G protein-coupled receptor (GPCR) superfamily. These agonists include peptide domains derived from the envelope proteins of human immunodeficiency virus type 1 (HIV-1) and at least three amyloidogenic polypeptides, the human acute phase protein serum amyloid A, the 42 amino acid form of beta amyloid peptide and a 21 amino acid fragment of human prion. Furthermore, a cleavage fragment of neutrophil granule-derived bactericidal cathelicidin, LL-37, is also a chemotactic agonist for FPRL1. Activation of formyl peptide receptors results in increased cell migration, phagocytosis, release of proinflammatory mediators, and the signaling cascade culminates in heterologous desensitization of other STM receptors including chemokine receptors CCR5 and CXCR4, two coreceptors for HIV-1. Thus, by interacting with a variety of exogenous and host-derived agonists, formyl peptide receptors may play important roles in proinflammatory and immunological diseases and constitute a novel group of pharmacological targets.

Animals↗

PubMed2002

Study on the relationship between NB4 cell apoptosis induced by tanshinone IIA and the cell mitochondrial transmembrane potential.

OBJECTIVE: To explore the relationship between NB4 cell apoptosis induced by tanshinone IIA (TanIIA) and the cell mitochondrial transmembrane potential (DeltaPsim). METHODS: NB4 cells were treated with TanIIA, As(2)O(3), TanIIA plus 1.0 micro g/ml CsA and As(2)O(3) plus 1.0 micro g/ml CsA, respectively. Morphological changes were observed under light microscope and transmission electron microscope. The percentages of sub-G(1) cells and DeltaPsim of cells doublely stained with PI and Rh123 were assayed by flow cytometry. RESULTS: The percentages of sub-G(1) cells after treatment with 1.0 micro g/ml and 2.0 micro g/ml TanIIA had no significant difference but was higher than that of 0.5 micro g/ml. After treatment with TanIIA, NB4 cells appeared the classical apoptotic morphology. The percentages of sub-G(1) cells were increased, while the DeltaPsim reduced (P < 0.01) and there was a linear correlation between them. The increment of sub-G(1) cell percentages and decrement of DeltaPsim induced by TanIIA were partly inhibited by CsA (P < 0.01). CONCLUSIONS: TanIIA can induce NB4 cells apoptosis through opening the mitochondrial permeability transition pore and reducing DeltaPSgr;m, and this effect could be inhibited by CsA.

Abietanes↗

PubMed2002

[The effect of interferon alone, cytosine arabinoside alone and their combined effect on hematopoietic progenitors of chronic myeloid leukemia in vitro].

OBJECTIVE: In order to search for more effective treatment regimen of chronic myeloid leukemia (CML). METHODS: Semisolid culture and conventional chromosome assay were used to evaluate the effect of interferon (IFN) and Ara-c on K562 cell line and BMMNCs from CML patients and normal controls. RESULTS: IFN had no obvious inhibitory effect on K562 cell. IFN and Ara-c had preferential inhibitory effect on CFU-GM growth of CML and selective cytotoxic effect on CML Ph+ cell. The combination of IFN with Ara-c enhanced the cytotoxic effect of IFN or Ara-c alone on CML cells. CONCLUSION: IFN and Ara-c can be selected for therapy of CML in chronic phase. The combination of IFN with Ara-c may be more effective than IFN or Ara-c alone for the therapy of CML.

Adult↗

PubMed2002

[Study on the differentiation of K562 cell-line induced by Tanshinone II A].

OBJECTIVE: To investigate the effect of Tanshinone II A on K562 cell-line and its possible mechanism. METHODS: Cell culture, cytomorphology and cytometrics were used. RESULTS: The proliferative inhibition of K562 cells induced by Tanshinone II A was dose-independent, and the degrees of erythroid differentiation induced by 30 nmol/L ACM and 0.5 microgram/ml Tanshinone II A were not statistically different (P > 0.05). CONCLUSION: Tanshinone II A has an inhibitive effect on the proliferation of K562 cells and an inductive effect on the differentiation of erythrocyte series. The mechanisms may be related to the changes of cell cycle and gene expressions.

Abietanes↗