Synthesis of a lipomannan component of the cell-wall complex of Mycobacterium tuberculosis is based on Paulsen's concept of donor/acceptor "match".
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Carbohydrate Sequence↗
Biomedical subjects
Jun Lu
Publications and source records attributed to Jun Lu.
Pathway level analysis of gene expression using singular value decomposition.
BACKGROUND: A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes). Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications. RESULTS: We demonstrate our approach using expression data from a study of type 2 diabetes and another of the influence of cigarette smoke on gene expression in airway epithelia. A number of interesting pathways are identified in comparisons between smokers and non-smokers including ones related to nicotine metabolism, mucus production, and glutathione metabolism. A comparison with results from the related approach, 'gene-set enrichment analysis', is also provided. CONCLUSION: Our method offers a flexible basis for identifying differentially expressed pathways from gene expression data. The results of a pathway-based analysis can be complementary to those obtained from one more focused on individual genes. A web program PLAGE (Pathway Level Analysis of Gene Expression) for performing the kinds of analyses described here is accessible at http://dulci.biostat.edu/pathways.
Blood Glucose↗
Movement suppression during anesthesia: neural projections from the mesopontine tegmentum to areas involved in motor control.
Microinjection of pentobarbital and GABA(A)-receptor agonists into a brainstem region we have called the mesopontine tegmental anesthesia area (MPTA; Devor and Zalkind [2001] Pain 94:101-112) induces a general anesthesia-like state. As in systemic general anesthesia, rats show loss of the righting reflex, atonia, nonresponsiveness to noxious stimuli, and apparent loss of consciousness. GABA(A) agonist anesthetics acting on the MPTA might suppress movement by engaging endogenous motor regulatory systems previously identified in research on decerebrate rigidity and REM sleep atonia. Anterograde and retrograde tracing revealed that the MPTA has multiple descending projections to pontine and medullary areas known to be associated with motor control and atonia. Prominent among these are the dorsal pontine reticular formation and components of the rostral ventromedial medulla (RVM). The MPTA also has direct projections to the intermediate gray matter and ventral horn of the spinal cord via the lateral and anterior funiculi. These projections show a rostrocaudal topography: neurons in the rostral MPTA project to the RVM, but only minimally to the spinal cord, while those in the caudal MPTA project to both targets. Finally, the MPTA has ascending projections to motor control areas including the substantia nigra, subthalamic nucleus, and the caudate-putamen. Projections are bilateral with an ipsilateral predominance. We propose that GABA(A) agonist anesthetics induce immobility at least in part by acting on these endogenous motor control pathways via the MPTA. Analysis of MPTA connectivity has the potential for furthering our understanding of the neural circuitry responsible for the various functional components of general anesthesia.
Anesthetics↗
A strategy for ready preparation of glycolipids for multivalent presentation.
The olefinic residue of n-pentenyl glycosides serves as the trigger for regioselective construction of higher saccharides and then for elaboration in multivalent glycolipids. [reaction: see text]
Alkenes↗
Kinetics of model energy landscapes: an approach to complex systems.
An idealized potential energy surface (PES), simply a PES-like network of stationary points, is demonstrated to be a useful tool to study kinetic relaxation of complex energy landscapes. Combined with a master equation, we show that if constructed with proper regularity, the kinetics of the PES is easy to predict and understand by carefully examining the eigenmodes of the master equation. By modifying the idealized PES model to make it more and more complicated, we demonstrate a systematic method to study the complex kinetics on large PES. The idealized PES model is used to explore the feasibility and the robustness of statistical sampling of large PES. We develop several sampling strategies, such as the "rough topography sampling" and the "low barrier saddle sampling" in the idealized PES model and find they are also applicable to a realistic PES of the 13-atom Morse cluster with range parameter rho= 6. To measure the robustness of the sampling methods, we compare the eigenvalue spectra, the eigenvector similarity and the relaxation times of the total energy of the full and sample PESs.
Algorithms↗
Abscisic acid-induced apoplastic H2O2 accumulation up-regulates the activities of chloroplastic and cytosolic antioxidant enzymes in maize leaves.
The histochemical and cytochemical localization of abscisic acid (ABA)-induced H(2)O(2) production in leaves of maize (Zea mays L.) plants were examined, using 3,3-diaminobenzidine (DAB) and CeCl(3) staining, respectively, and the relationship between ABA-induced H(2)O(2) production and ABA-induced subcellular activities of antioxidant enzymes was studied. H(2)O(2) generated in response to ABA treatment was detected within 0.5 h in major veins of the leaves and maximized at about 2-4 h. In mesophyll and bundle sheath cells, ABA-induced H(2)O(2) accumulation was observed only in apoplast, and the greatest accumulation occurred in the walls of mesophyll cells facing large intercellular spaces. Meanwhile, ABA treatment led to a significant increase in the activities of the leaf chloroplastic and cytosolic antioxidant enzymes superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione reductase (GR), and pretreatment with the NADPH oxidase inhibitor diphenyleneiodonium (DPI), the O (2) (-) scavenger Tiron and the H(2)O(2) scavenger dimethylthiourea (DMTU) almost completely arrested the increase in the activities of these antioxidant enzymes. Our results indicate that the accumulation of apoplastic H(2)O(2) is involved in the induction of the chloroplastic and cytosolic antioxidant enzymes. Moreover, an oxidative stress induced by paraquat (PQ), which generates O (2) (-) and then H(2)O(2) in chloroplasts, also up-regulated the activities of the chloroplastic and cytosolic antioxidant enzymes, and the up-regulation was blocked by the pretreatment with Tiron and DMTU. These data suggest that H(2)O(2) produced at a specific cellular site could coordinate the activities of antioxidant enzymes in different subcellular compartments.
3,3'-Diaminobenzidine↗
A Munc13/RIM/Rab3 tripartite complex: from priming to plasticity?
alpha-RIMs and Munc13s are active zone proteins that control priming of synaptic vesicles to a readily releasable state, and interact with each other via their N-terminal sequences. The alpha-RIM N-terminal sequence also binds to Rab3s (small synaptic vesicle GTPases), an interaction that regulates presynaptic plasticity. We now demonstrate that alpha-RIMs contain adjacent but separate Munc13- and Rab3-binding sites, allowing formation of a tripartite Rab3/RIM/Munc13 complex. Munc13 binding is mediated by the alpha-RIM zinc-finger domain. Elucidation of the three-dimensional structure of this domain by NMR spectroscopy facilitated the design of a mutation that abolishes alpha-RIM/Munc13 binding. Selective disruption of this interaction in the calyx of Held synapse decreased the size of the readily releasable vesicle pool. Our data suggest that the ternary Rab3/RIM/Munc13 interaction approximates synaptic vesicles to the priming machinery, providing a substrate for presynaptic plasticity. The modular architecture of alpha-RIMs, with nested binding sites for Rab3 and other targets, may be a general feature of Rab effectors that share homology with the alpha-RIM N-terminal sequence.
Amino Acid Sequence↗
Enantioselective allylation of ketones catalyzed by chiral In(III)-PYBOX complexes.
In the presence of 20 mol% of chiral catalytic complex prepared from In(OTf)3 and chiral PYBOX, allyltributylstannane reacted with achiral ketones to afford the corresponding homoallylic alcohols in moderate to high enantioselectivities (54-95% ee), which constitutes the first example of enantioselective allylation of ketones catalyzed by the chiral In(III)-PYBOX complex.
Journal Article↗
Interleukin-12 p40 promoter activity is regulated by the reversible acetylation mediated by HDAC1 and p300.
Interleukin-12 (IL-12) is a heterodimeric cytokine produced by macrophages in response to intracellular pathogens. The importance of IL-12 in generation of Th1 response against human pathogens has been characterized. The coactivator p300 is an important histone acetyltransferase (HAT) and has been implicated in the regulation of many genes. Histone deacetylases (HDACs) regulate gene transcription through deacetylation of histones. Whether the reversible histone acetylation/deacetylation modification participates in the regulation of IL-12 p40 transcription expression has not been investigated before. In this study, we analyzed the roles of HDAC1 and p300 in the regulation of human IL-12 p40. Co-transfection studies showed that HDAC1 had a repressing effect on the activity of IL-12 p40 promoter. Contrarily, p300 was able to reinforce the C/EBPbeta-mediated activation of IL-12 p40 and it counteracted the HDAC1-mediated repression of the IL-12 promoter. Chromatin immunoprecipitation tests (ChIP) revealed that p300 had a stimulating effect on the acetylation of the histone H3 at IL-12 p40 promoter. In addition, we showed that p300 had a physical interaction with C/EBPbeta and can enhance acetylation of C/EBPbeta. Data presented in this paper indicate that the reversible histone acetylation/deacetylation modification plays an important role in the transcriptional regulation of IL-12.
Acetylation↗
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach.
BACKGROUND: In testing for differential gene expression involving multiple serial analysis of gene expression (SAGE) libraries, it is critical to account for both between and within library variation. Several methods have been proposed, including the t test, tw test, and an overdispersed logistic regression approach. The merits of these tests, however, have not been fully evaluated. Questions still remain on whether further improvements can be made. RESULTS: In this article, we introduce an overdispersed log-linear model approach to analyzing SAGE; we evaluate and compare its performance with three other tests: the two-sample t test, tw test and another based on overdispersed logistic linear regression. Analysis of simulated and real datasets show that both the log-linear and logistic overdispersion methods generally perform better than the t and tw tests; the log-linear method is further found to have better performance than the logistic method, showing equal or higher statistical power over a range of parameter values and with different data distributions. CONCLUSION: Overdispersed log-linear models provide an attractive and reliable framework for analyzing SAGE experiments involving multiple libraries. For convenience, the implementation of this method is available through a user-friendly web-interface available at http://www.cbcb.duke.edu/sage.
Carcinoma, Pancreatic Ductal↗
MicroRNA expression profiles classify human cancers.
Recent work has revealed the existence of a class of small non-coding RNA species, known as microRNAs (miRNAs), which have critical functions across various biological processes. Here we use a new, bead-based flow cytometric miRNA expression profiling method to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers. The miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours. We observe a general downregulation of miRNAs in tumours compared with normal tissues. Furthermore, we were able to successfully classify poorly differentiated tumours using miRNA expression profiles, whereas messenger RNA profiles were highly inaccurate when applied to the same samples. These findings highlight the potential of miRNA profiling in cancer diagnosis.
Animals↗
Ni11As8 single-crystalline nanosheets via hydrothermal redox route.
Ni11As8 crystallites 23-nm thick and 250-700-nm wide in lateral dimension were prepared in alkaline hydrothermal condition. Transmission electron microscope (TEM) images and selected area electron diffraction (SAED) analyses showed that the as-prepared Ni11As8 was single-crystalline nanosheets of [331] orientation. The Ni11As8 exhibited an optical absorption onset of 3.00 eV in the visible spectral regime. Its magnetic measurement indicated a weak magnetic hysteresis and unsaturation magnetization with a magnetic susceptibility of 1.37 x 10(-4) cm3/g (at 15 kOe) at room temperature, the origin of which was discussed and assigned to the effect of surface species containing Ni ions. The extended Hückel tight-binding calculation revealed that bulk Ni11As8 has a 3d-localized narrow band below Fermi level and complicated band structure with small band gap in the first Brillouin zone, which supply clues to explain the observed optical and magnetic properties. The formation mechanism of Ni11As8 was studied and attributed to an alkaline hydrothermal redox route on the basis of the Marsh reaction.
Journal Article↗
Thioredoxin reductase is irreversibly modified by curcumin: a novel molecular mechanism for its anticancer activity.
The thioredoxin reductase (TrxR) isoenzymes, TrxR1 in cytosol or nucleus and TrxR2 in mitochondria, are essential mammalian selenocysteine (Sec)-containing flavoenzymes with a -Gly-Cys-Sec-Gly active site. TrxRs are the only enzymes catalyzing the NADPH-dependent reduction of the active site disulfide in thioredoxins (Trxs), which play essential roles in substrate reductions, defense against oxidative stress, and redox regulation by thiol redox control. TrxRs have been found to be overexpressed by a number of human tumors. Curcumin, which is consumed daily by millions of people, is a polyphenol derived from the plant Curcuma longa. This phytochemical has well known anticancer and antiangiogenic properties. In this study we report that rat TrxR1 activity in Trx-dependent disulfide reduction was inhibited by curcumin. The IC(50) value for the enzyme was 3.6 microM after incubation at room temperature for 2 h in vitro. The inhibition occurred with enzyme only in the presence of NADPH and persisted after removal of curcumin. By using mass spectrometry and blotting analysis, we proved that this irreversible inhibition by curcumin was caused by alkylation of both residues in the catalytically active site (Cys(496)/Sec(497)) of the enzyme. However, the curcumin-modified enzyme showed a strongly induced NADPH oxidase activity to produce reactive oxygen species. Inhibition of TrxR by curcumin added to cultured HeLa cells was also observed with an IC(50) of around 15 microM. Modification of TrxR by curcumin provides a possible mechanistic explanation for its cancer preventive activity, shifting the enzyme from an antioxidant to a prooxidant.
Animals↗
Determination of phenazopyridine in human plasma via LC-MS and subsequent development of a pharmacokinetic model.
This paper describes a new LC-MS method for the determination of phenazopyridine and the subsequent development of a pharmacokinetic model for phenazopyridine in vivo. Phenazopyridine hydrochloride is a strong analgesic used in the treatment of urinary tract infections. Although it has been used as a clinical treatment for a very long time, pharmacokinetic data and suitable methods for its determination in plasma are currently lacking. The study described in this paper used high performance liquid chromatography-mass spectrometry, HPLC-MS, to determine the plasma concentrations of phenazopyridine in human subjects after oral administration. After liquid-liquid extraction, the phenazopyridine in the plasma was analyzed on a C18 column under SIM mode. A double-peak phenomenon was observed in most of the concentration-time profiles of the subjects. Although some drugs are known to cause this phenomenon, phenazopyridine has not been reported to do so. Several possible causes were analyzed in order to obtain an explanation. We proposed a two-site absorption compartment model to fit the concentration data in vivo, which has one more absorption site than the classical one-compartment model. The model describes the concentration profiles in different dose groups well and could provide an explanation for the double-peak phenomenon. The three dose groups exhibited similar model parameters and a linear pharmacokinetic process over the dose range used.
Area Under Curve↗
The Elp3 subunit of human Elongator complex is functionally similar to its counterpart in yeast.
Functions of the Elp3 subunit of the recently purified human Elongator were studied using an in vivo yeast complementation system. We demonstrated that the human ELP3 gene (hELP3) was able partially to complement functional defects of yeast elp3Delta cells. Furthermore, a chimeric ELP3 gene (yhELP3) encoding a protein in which the putative histone acetyltransferase (HAT) domain of hELP3 fused to the remainder of the yeast Elp3p corrected the growth defects of elp3Delta cells and complemented the slow activation of some inducible genes. Moreover, deletion of the B motif of the catalytic domain of the HAT region of hELP3 eliminated the ability of yhELP3 to complement elp3Delta in vivo, indicating that the HAT activity is essential for ELP3 function. We also demonstrated that replacement of specific lysine residues in histones H3 and H4 by arginine affected the complementation capacity of both the yeast gene (yELP3) and the chimeric yhELP3 in the elp3Deltastrain. Specifically, mutation of lysine-14 of H3 (H3 K14R) or lysine-8 of H4 (H4 K8R) reduced the ability of yELP3 and yhELP3 to complement the elp3Delta mutant, whereas simultaneous mutation of both sites (H3 K14R/H4 K8R) almost completely abolished complementation. These results imply a link between the acetylation of specific sites in nucleosomal histones and the regulation of transcription elongation by human Elp3. The data presented in this report suggest that the Elp3 subunits of human and yeast are highly conserved in their structure and functions.
Acetyltransferases↗
Preferential suppression of trisomy 8 compared with normal hematopoietic cell growth by autologous lymphocytes in patients with trisomy 8 myelodysplastic syndrome.
Clinical observations and experimental evidence link bone marrow failure in myelodysplastic syndrome (MDS) with a T cell-dominated autoimmune process. Immunosuppressive therapy is effective in improving cytopenias in selected patients. Trisomy 8 is a frequent cytogenetic abnormality in bone marrow cells in patients with MDS, and its presence has been associated anecdotally with good response to immunotherapy. We studied 34 patients with trisomy 8 in bone marrow cells, some of whom were undergoing treatment with antithymocyte globulin (ATG). All had significant CD8+ T-cell expansions of one or more T-cell receptor (TCR) Vbeta subfamilies, as measured by flow cytometry; expanded subfamilies showed CDR3 skewing by spectratyping. Sorted T cells of the expanded Vbeta subfamilies, but not of the remaining subfamilies, inhibited trisomy 8 cell growth in short-term hematopoietic culture. The negative effects of Vbeta-expanded T cells were inhibited by major histocompatibility complex (MHC) class 1 monoclonal antibody (mAb) and Fas antagonist and required direct cell-to-cell contact. Sixty-seven percent of patients who had de novo MDS with trisomy 8 as the sole karyotypic abnormality responded to ATG with durable reversal of cytopenias and restoration of transfusion independence, with stable increase in the proportion of trisomy 8 bone marrow cells and normalization of the T-cell repertoire. An increased number of T cells with apparent specificity for trisomy 8 cells is consistent with an autoimmune pathophysiology in trisomy 8 MDS.
Adult↗
Histone acetyltransferase p300 promotes the activation of human WT1 promoter and intronic enhancer.
The Wilms' tumor gene-1 (WT1) encodes a zinc finger protein involved in gene regulation during kidney, gonad, and heart development. In addition to its promoter, a 258 bp intronic enhancer is required for tissue-specific expression of WT1 gene. p300 is a histone acetyltransferase (HAT) and exerts essential functions in gene regulation. Here, we show that p300 increased the expression of endogenous WT1 mRNA and promoted the activation of the WT1 promoter and intronic enhancer. The results also revealed that the adenovirus E1A repressed the p300 function, while the p300-binding defective E1A delta 2-36 did not, and p300 HAT activity was important for its function since p300 mutant with the HAT domain deleted partially abrogated its ability to activate the WT1 promoter and intronic enhancer. Furthermore, p300 and c-Myb synergistically activated the expression of WT1 gene. This study revealed that p300 and its HAT activity were involved in regulation of WT1 transcription.
Acetyltransferases↗
Enantioselective allylation of aldehydes catalyzed by chiral indium(III) complexes immobilized in ionic liquids.
In the presence of chiral catalytic complexes prepared from In(OTf)3 and chiral PYBOX ligands, allytributylstannane reacted with aldehydes in ionic liquids to afford the corresponding homoallylic alcohols in high enantioselectivities (86-94% ee) and good yields (68-89%); the chiral catalysts immobilized in ionic liquids could be reused with comparable enantioselectivities and yields.
Alcohols↗