Biomedical subjects

D Chen

Publications and source records attributed to D Chen.

At least 37 records · Page 2Linked to original sources

PubMed2005

What the Aspergillus genomes have told us.

The sequencing and annotation of the genomes of the first strains of Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus will be seen in retrospect as a transformational event in Aspergillus biology. With this event the entire genetic composition of A. nidulans, the sexual experimental model organism of the genus Aspergillus, A. oryzae, the food biotechnology organism which is the product of centuries of cultivation, and A. fumigatus, the most common causative agent of invasive aspergillosis is now revealed to the extent that we are at present able to understand. Each genome exhibits a large set of genes common to the three as well as a much smaller set of genes unique to each. Moreover, these sequences serve as resources providing the major tool to expanding our understanding of the biology of each. Transcription profiling of A. fumigatus at high temperatures and comparative genomic hybridization between A. fumigatus and a closely related Aspergillus species provides microarray based examples of the beginning of functional analysis of the genomes of these organisms going forward from the genome sequence.

Aspergillosis↗

PubMed2005

Manganese (IV) oxide-catalyzed electrophilic diamination of electron-deficient alkenes provides an easy synthesis of alpha,beta-diamino acid and ketone derivatives for peptidomimetic studies.

Manganese (IV) oxide was found to catalyze the diamination reaction of alpha,beta-unsaturated esters and ketones with N,N-dichloro-p-toluenesulfonamide and acetonitrile as the halogen and nitrogen sources. The reaction is convenient to be conducted by simply mixing three reactants in the presence of manganese dioxide catalyst and 4 A molecular sieves, and provides an easy access to 1-p-toluenesulfonyl-3-trichloromethyl-4,5-imidazoline derivatives, which are useful building blocks for peptidomimetic studies.

Alkenes↗

PubMed2005

Identification of secret agent as the O-GlcNAc transferase that participates in Plum pox virus infection.

Serine and threonine of many nuclear and cytoplasmic proteins are posttranslationally modified with O-linked N-acetylglucosamine (O-GlcNAc). This modification is made by O-linked N-acetylglucosamine transferases (OGTs). Genetic and biochemical data have demonstrated the existence of two OGTs of Arabidopsis thaliana, SECRET AGENT (SEC) and SPINDLY (SPY), with at least partly overlapping functions, but there is little information on their target proteins. The N terminus of the capsid protein (CP) of Plum pox virus (PPV) isolated from Nicotiana clevelandii is O-GlcNAc modified. We show here that O-GlcNAc modification of PPV CP also takes place in other plant hosts, N. benthamiana and Arabidopsis. PPV was able to infect the Arabidopsis OGT mutants sec-1, sec-2, and spy-3, but at early times of the infection, both rate of virus spread and accumulation were reduced in sec-1 and sec-2 relative to spy-3 and wild-type plants. By matrix-assisted laser desorption ionization-time of flight mass spectrometry, we determined that a 39-residue tryptic peptide from the N terminus of CP of PPV purified from the spy-3 mutant, but not sec-1 or sec-2, was O-GlcNAc modified, suggesting that SEC but not SPY modifies the capsid. While our results indicate that O-GlcNAc modification of PPV CP by SEC is not essential for infection, they show that the modification has a role(s) in the process.

Acylation↗

PubMed2005

Therapeutic potential of peptide deformylase inhibitors.

Peptide deformylase (PDF) is an attractive target for antibacterial drug discovery. Progress in the biological characterisation of the enzyme, coupled with newly obtained mechanistic and structural insight, enabled the pharmaceutical industry to discover potent PDF inhibitors that can be considered as clinical development candidates for this new class of antibacterial agents. The in vitro and in vivo data for several lead PDF inhibitors suggest that the current PDF inhibitors are most suitable for the treatment of respiratory tract infections and they are not cross-resistant to the current clinically used antibiotics. Two PDF inhibitors, BB-83698 and VIC-104959, have progressed to Phase I clinical trials by intravenous and oral administration, respectively. Both of these compounds show promising in vitro and in vivo efficacy and an excellent safety profile. The pharmacokinetics in humans for both of the compounds suggest the possibility of a twice-daily dosing regimen for clinical use. Thus far, all of the data suggest a promising future for this new class of antibacterial agents.

Amidohydrolases↗

PubMed2005

Bacterial Peptide deformylase inhibitors: a new class of antibacterial agents.

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth but is not required by mammalian cells. Thus, it represents a selective and promising target for the development of new antibacterial agents. Since deformylase inhibitors have yet to be used clinically as antibacterial drugs, compounds targeting this enzyme should avoid cross-resistance with currently used antibacterial agents. The PDF enzyme is a ferrous ion-containing metallohydrolase, but a nickel-containing surrogate is routinely used in the laboratory for testing inhibitors due to its better stability. Enzymes from several bacterial species have been cloned and both their three-dimensional structures and co-crystal structures with bound inhibitor have been determined. As a metallo enzyme, PDF lends itself to the well-precedented mechanism-based rational drug design approach. Using structural and mechanistic information together with high throughput screening, several types of potent PDF inhibitors have been identified. PDF inhibitors identified to date share a common structural feature of a "chelator + peptidomimetic" scaffold. Although compounds with many different chelators inhibit the cell free enzyme, only compounds containing hydroxamic acid or N-formyl hydroxylamine exhibit appreciable antibacterial activity. Several lead inhibitors have demonstrated in vivo efficacy and an excellent safety profile. Two PDF inhibitors, VIC-104959 (LBM415) and BB-83698, have progressed to Phase I clinical trials. In this review, different PDF inhibitors are compared and their biological activities are discussed. Structure-activity relationships have been established and the implications of this work in the design of future PDF inhibitors are considered.

Amidohydrolases↗

PubMed2004

Rainbow: a toolbox for phylogenetic supertree construction and analysis.

UNLABELLED: Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced. Rainbow is available for Mac OS X, Windows and Linux. AVAILABILITY: Rainbow is a free open-source software. Its binary files, source code, and manual can be downloaded from the Rainbow web page: http://genome.cs.iastate.edu/Rainbow/

Algorithms↗

PubMed2004

Interleukin-1 gene cluster polymorphisms and risk of Alzheimer's disease in Chinese Han population.

Interleukin-1 (IL-1) has been implicated as a key cytokine in Alzheimer's disease (AD) pathogenesis. IL-1 gene polymorphisms, especially IL-1A C((-)889)T polymorphism, have been suggested to be associated with AD risk and onset age. To determine if IL-1 polymorphisms are genetic risk factors for developing AD in Chinese Mainland population, we analyzed IL-1A ((-)889), IL-1B ((-)511) and IL-1RN variable number of tandem repeat (VNTR) polymorphisms in a sample of 145 sporadic AD patients and 181 healthy controls. Our data revealed that the three polymorphisms in IL-1 gene cluster might not play a key role in AD pathogenesis in Chinese Mainland Han population.

Age of Onset↗

PubMed2004

Histamine and histidine decarboxylase are hallmark features of ECL cells but not G cells in rat stomach.

The oxyntic mucosa of the rat stomach is rich in ECL cells which produce and secrete histamine in response to gastrin. Histamine and the histamine-forming enzyme histidine decarboxylase (HDC) have been claimed to occur also in the gastrin-secreting G cells in the antrum. In the present study, we used a panel of five HDC antisera and one histamine antiserum to investigate whether histamine and HDC are exclusive to the ECL cells. By immunocytochemistry, we could show that the ECL cells were stained with the histamine antiserum and all five HDC antisera. The G cells, however, were not stained with the histamine antiserum, but with three of the five HDC antisera. Thus, histamine and HDC coexist in the ECL cells (oxyntic mucosa) but not in G cells (antral mucosa). Western blot analysis revealed a typical pattern of HDC-immunoreactive bands (74, 63 and 54 kDa) in oxyntic mucosa extracts with all five antisera. In antral extracts, immunoreactive bands were detected with three of the five HDC antisera (same as above); the pattern of immunoreactivity differed from that in oxyntic mucosa. Food intake of fasted rats or treatment with the proton pump inhibitor omeprazole raised the HDC activity and the HDC protein content of the oxyntic mucosa but not of the antral mucosa; the HDC activity in the antrum was barely detectable. We suggest that the HDC-like immunoreactivity in the antrum represents a cross-reaction with non-HDC proteins and conclude that histamine and HDC are hallmark features of ECL cells but not of G cells.

Animals↗

PubMed2004

Global gene expression of fission yeast in response to cisplatin.

The cellular response to the antitumor drug cisplatin is complex, and resistance is widespread. To gain insights into the global transcriptional response and mechanisms of resistance, we used microarrays to examine the fission yeast cell response to cisplatin. In two isogenic strains with differing drug sensitivity, cisplatin activated a stress response involving glutathione-S-transferase, heat shock, and recombinational repair genes. Genes required for proteasome-mediated protein degradation were up-regulated in the sensitive strain, whereas genes for DNA damage recognition/repair and for mitotic progression were induced in the resistant strain. The response to cisplatin overlaps in part with the responses to cadmium and the DNA-damaging agent methylmethane sulfonate. The different gene groups involved in the cellular response to cisplatin help the cells to tolerate and repair DNA damage and to overcome cell cycle blocks. These findings are discussed with respect to known cisplatin response pathways in human cells.

Antineoplastic Agents↗

PubMed2004

MEPE has the properties of an osteoblastic phosphatonin and minhibin.

Matrix extracellular phosphoglycoprotein (MEPE) is expressed exclusively in osteoblasts, osteocytes and odontoblasts with markedly elevated expression found in X-linked hypophosphatemic rickets (Hyp) osteoblasts and in oncogenic hypophosphatemic osteomalacia (OHO) tumors. Because these syndromes are associated with abnormalities in mineralization and renal phosphate excretion, we examined the effects of insect-expressed full-length human-MEPE (Hu-MEPE) on serum and urinary phosphate in vivo, (33)PO(4) uptake in renal proximal tubule cultures and mineralization of osteoblast cultures. Dose-dependent hypophosphatemia and hyperphosphaturia occurred in mice following intraperitoneal (IP) administration of Hu-MEPE (up to 400 microg kg(-1) 31 h(-1)), similar to mice given the phosphaturic hormone PTH (80 microg kg(-1) 31 h(-1)). Also the fractional excretion of phosphate (FEP) was stimulated by MEPE [65.0% (P < 0.001)] and PTH groups [53.3% (P < 0.001)] relative to the vehicle group [28.7% (SEM 3.97)]. In addition, Hu-MEPE significantly inhibited (33)PO(4) uptake in primary human proximal tubule renal cells (RPTEC) and a human renal cell line (Hu-CL8) in vitro (V(max) 53.4% inhibition; K(m) 27.4 ng/ml, and V(max) 9.1% inhibition; K(m) 23.8 ng/ml, respectively). Moreover, Hu-MEPE dose dependently (50-800 ng/ml) inhibited BMP2-mediated mineralization of a murine osteoblast cell line (2T3) in vitro. Inhibition of mineralization was localized to a small (2 kDa) cathepsin B released carboxy-terminal MEPE peptide (protease-resistant) containing the acidic serine-aspartate-rich motif (ASARM peptide). We conclude that MEPE promotes renal phosphate excretion and modulates mineralization.

Amino Acid Sequence↗

PubMed2004

A study of HLA-G1 protection of porcine endothelial cells against human NK cell cytotoxicity.

UNLABELLED: Human natural killer (NK) cells, which can directly lyse porcine endothelial cells, play an important role in xenotransplantation. HLA-G is a nonclassical major histocompatibility complex (MHC) class I molecules that has been implicated in protecting susceptible target cells from lysis by NK cells. The objective was to study the effect of protecting porcine endothelial cells transfected with HLA-G1 from human NK cell lysis. METHODS: The recombinant expression vector pcDNA3-HLA-G1 was transfected into primary cultured porcine aortic endothelial cells (PAECs) by lipofection. Surface expression of HLA-G1 in transected PAECs was confirmed by an immunofluoresence technique. Peripheral blood mononuclear cells (PBMC) and NK cell line (NK92) were used as NK effects cells with pcDNA3-HLA-G1-transfected PAECs as targets in a MTT method using pcDNA3 transfection as a negative control. RESULTS: Expression of HLA-G1 on PAECs conferred significant protection against NK-mediated lysis. The rate of NK92 cytotoxicity was reduced to 41.5% +/- 14.0% from 75.3% +/- 10.5% in the control group (P < .01). Similarly the rate of the PBMC cytotoxicity among different donors (n = 7) was reduced to 45.4% +/- 12.1% in contrast to 74.6% +/- 11.2% in the control group (P < .05). CONCLUSIONS: HLA-G1 molecules can directly protect xenogeneic PAECs against attack by human NK cells. These results indicate that the expression of HLA-G1 on the porcine cell surface may provide a new approach to overcome NK-mediated immunity to xenografts.

Animals↗

PubMed2004

Pathogenesis and pathology of delayed xenograft rejection in pig-to-rhesus monkey cardiac transplantation.

UNLABELLED: It has been recognized that delayed xenograft rejection (DXR) is the major barrier to the acceptance of xenotransplantation after overcoming hyperacute rejection. OBJECTIVES: This study sought to investigate the pathogenesis and pathology of delayed xenograft rejection following pig-to-rhesus monkey heart xenotransplantation. METHODS: Heterotopic xenogeneic heart transplants in the abdominal cavity were performed using piglet donors to four monkey recipients. Complete complement depletion was achieved in the recipients with repetitive doses of high-activity cobra venom factor (Y-CVF). The recipients were immunosuppressed with a combination of cyclosporine, cyclophosphamide, and steroids. Sera were analyzed for C3 and C4 levels and complement activity and anti-pig endothelial xenoantibody. The grafts were examined histopathologically and immunohistochemically for C3, C4;C5b-9, IgM, IgG, tumor necrosis factor-alpha (TNF-alpha), intercellular adhesion molecule-1(ICAM-1), CD57(NK cells), CD68 (macrophages), CD4, and CD8. RESULTS: Xenografts survived 8, 10, 13, and 13 days respectively, all developing DXR. Venous thrombosis was the outstanding feature within DXR xenografts, complicated by interstitial edema, local hemorrhage, myocardial necrosis, and mild to moderate cellular infiltration. The serum C3 levels and complement activity decreased to almost 0 from the day of transplantation due to treatment with Y-CVF. The C4 level began to decrease 2 to 4 days before the cardiac xenografts lost their function. Anti-pig endothelial xenoantibody also decreased after transplantation, slightly increasing during DXR. All rejected xenografts showed C3, C4, C5b-9, IgG, and IgM deposits to various degrees. Large numbers of macrophages (50% of total leukocytes) infiltrated the entire xenograft with a few natural killer cells (8% to 10%), as well as some CD4+ T cells (15%) and CD8+ T cells (25%). Upregulation of ICAM-1 on graft endothelial cells and TNF-alpha in the interstitium were also demonstrated in the rejected heart. CONCLUSION: Both humoral and cell-mediated immunologic reactions may play important roles in the pathogenesis of DXR. Besides C3, C4, C5b-9, IgM, and IgG destroying the xenograft, NK cells, macrophages, and CD4+ and CD8+ T cells may further aggravate the development of DXR.

Animals↗

PubMed2004

Radiation fields in gynecologic oncology: correlation of soft tissue (surgical) to radiologic landmarks.

OBJECTIVES: (1). To determine if radiation fields defined by bony structure landmarks correlate to anatomic boundaries of lymph node dissection marked intraoperatively; and (2). to determine if a patient's body mass index (BMI) correlates with these anatomic or radiographic boundaries. METHODS: One hundred patients undergoing exploratory laparotomy with pelvic and paraaortic lymph node dissection had three medium hemoclips placed at vascular junctions considered of clinical significance to lymph node dissection: insertion of the left ovarian vein into the renal vein, insertion of the right ovarian vein into the vena cava, inferior mesenteric artery (IMA), bifurcation of the aorta, bifurcation of the common iliacs (bilateral), and the insertion of the deep circumflex vein (DCV) in to the external iliac vein (bilateral). Postoperatively, an abdominal X-ray was obtained. Comparisons were made between these eight major vascular landmarks and radiographic bony landmarks that are used to define radiation field boundaries. The percentage of vascular landmarks that were encompassed or fell outside of traditional radiation fields was determined with a 1-cm margin considered an adequate boundary for radiation. These measurements were also compared to patient BMIs. RESULTS: Radiation fields defined by traditional bony landmarks would adequately encompass the paraaortic lymph nodes in the majority of patients (91%). For pelvic radiation fields, there was a significant "miss" (39%) of common iliac lymph nodes. Approximately one quarter (26%) of patients would receive inadequate coverage of one or both of the lateral boundaries of pelvic radiation. There was no apparent correlation of BMI to vascular or bony landmarks. CONCLUSIONS: Radiation fields determined by traditional bony landmarks do not adequately reflect the anatomic (surgical) landmarks associated with the lymphatic drainage of the female reproductive organs. Although the majority of tertiary care centers now use advanced imaging techniques (e.g. computed tomography) to plan their radiation treatments, the historical guidelines of radiographic landmarks are still used in smaller institutions and continue to be referenced in Gynecologic Oncology Group protocols. For centers still using radiographic landmarks, the application of hemoclips with X-ray identification is a low-cost modality that is easily reproducible and may be clinically useful in guiding treatment.

Adult↗

PubMed2004

A comparative study of quantitative structure-activity relationship methods based on gallic acid derivatives.

By using hologram quantitative structure-activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) methods, the relationships between the structures of 49 gallic acid derivatives and their analgesic activity have been investigated to yield statistically reliable models with considerable predictive power. The best HQSAR model was generated using atoms, bond and connectivity as fragment distinction parameters and fragment size 5-7 from a hologram length of 307 with 3 components. High conventional r2 (r2 = 0.825) and cross-validation r2 (r2(cv) = 0.726) values were obtained. CoMFA analyses varying lattice size and location, grid spacing, probe charges and using, Tripos standard and Indicator force field were performed. The best model was developed with 4 components using sp3-hybridized carbon atom with +1.0 charge as probe, grid spacing (2 A), lattice offset (1.0, 3.0, -2.5). The CoMFA model showed a conventional correlation coefficient r2 of 0.889 and across-validation r2(cv) equals to 0.633. The robustness and predictive ability of the HQSAR and CoMFA models have been validated by means of an external test set. The results indicate that both models possess high statistical quality in the prediction of analgesic potency of novel gallic acid analogs.

Forecasting↗

PubMed2004

Peptide deformylase inhibitors as antibacterial agents: identification of VRC3375, a proline-3-alkylsuccinyl hydroxamate derivative, by using an integrated combinatorial and medicinal chemistry approach.

Peptide deformylase (PDF), a metallohydrolase essential for bacterial growth, is an attractive target for use in the discovery of novel antibiotics. Focused chelator-based chemical libraries were constructed and screened for inhibition of enzymatic activity, inhibition of Staphylococcus aureus growth, and cytotoxicity. Positive compounds were selected based on the results of all three assays. VRC3375 [N-hydroxy-3-R-butyl-3-(2-S-(tert-butoxycarbonyl)-pyrrolidin-1-ylcarbonyl)propionamide] was identified as having the most favorable properties through an integrated combinatorial and medicinal chemistry effort. This compound is a potent PDF inhibitor with a K(i) of 0.24 nM against the Escherichia coli Ni(2+) enzyme, possesses activity against gram-positive and gram-negative bacterial pathogens, and has a low cytotoxicity. Mechanistic experiments demonstrate that the compound inhibits bacterial growth through PDF inhibition. Pharmacokinetic studies of this drug in mice indicate that VRC3375 is orally bioavailable and rapidly distributed among various tissues. VRC3375 has in vivo activity against S. aureus in a murine septicemia model, with 50% effective doses of 32, 17, and 21 mg/kg of body weight after dosing by intravenous (i.v.), subcutaneous (s.c.), and oral (p.o.) administration, respectively. In murine single-dose toxicity studies, no adverse effects were observed after dosing with more than 400 mg of VRC3375 per kg by i.v., p.o., or s.c. administration. The in vivo efficacy and low toxicity of VRC3375 suggest the potential for developing this class of compounds to be used in future antibacterial drugs.

Algorithms↗

PubMed2004

Increased pulmonary arterial pressure in children with nephrotic syndrome.

AIMS: To evaluate the pulmonary arterial pressure in children with nephrotic syndrome (NS). METHODS: Doppler echocardiography was performed in 40 children with NS (aged 1.5-13 years) at NS onset (n = 28) or relapse (n = 12), and 40 normal controls. Pulmonary pressure was estimated by: (1) measuring the systolic transtricuspid gradient from tricuspid regurgitation; and (2) measuring the time to peak velocity of pulmonary flow. RESULTS: Thirty five of the 40 patients with NS had measurable tricuspid regurgitation with a pulmonary systolic pressure ranging from 21 to 48 mm Hg. Pulmonary systolic pressure was >40 mm Hg in seven patients. The pulmonary time to peak velocity was shortened and the ratio of time to peak velocity and right ventricular ejection time decreased compared with controls. The patients with increased pulmonary pressure had a longer time since onset of NS. One patient developed thrombus in the inferior vena cava during hospitalisation. CONCLUSION: Pulmonary arterial pressure was increased in children with NS. Further work is needed to evaluate the aetiology and clinical implications of this abnormality.

Adolescent↗

PubMed2004

Effect of high-level natural radiation on chromosomes of residents in southern China.

To study the effect of low-dose (rate) radiation on human health, we analyzed chromosomes of peripheral lymphocytes of residents in a high background radiation area (HBRA) and compared the results with those obtained from residents in a control area (CA) in Guangdong Province, China. Unstable types of chromosome aberrations (dicentrics and rings) were studied in 22 members of eight families in HBRA and 17 members of five families in CA. Each family consists of three generations. On average 2,600 cells per subject were analyzed. 27 adults and six children in HBRA and 25 adults and eight children in CA were studied with respect to translocations. On average 4,741 cells per subject were examined. We found an increase of the frequency of dicentrics and rings in HBRA, where the natural radiation level is three to five times higher than in the control area. But the increase of translocations in HBRA was within the range of individual variation in the controls.

Adult↗

PubMed2003

Alpha-substituted hydroxamic acids as novel bacterial deformylase inhibitor-based antibacterial agents.

We report the synthesis and biological activity of analogues of VRC3375 (N-hydroxy-3-R-butyl-3-[(2-S-(tert-butoxycarbonyl)-pyrrolidin-1-ylcarbonyl]propionamide), an orally active peptide deformylase inhibitor. This study explores the structure-activity relationship of various chelator groups, alpha substituents, P(2)' and P(3)' substituents in order to achieve optimal antibacterial activity with minimal toxicity liability.

Amidohydrolases↗