Biomedical subjects

H Fang

Publications and source records attributed to H Fang.

At least 19 recordsLinked to original sources

PubMed2007

Emergence of VanD-type vancomycin-resistant Enterococcus faecium in Stockholm, Sweden.

A vancomycin-resistant Enterococcus faecium isolate from the urine of a liver transplant patient in Stockholm was found to contain a vanD gene. The sequence of the vanD PCR product shared 100% identity with the vanD5 allele. The isolate was resistant to a relatively high level of vancomycin (128 mg/L) and a low level of teicoplanin (4 mg/L). This is the first VanD-type vancomycin-resistant E. faecium isolate reported in Sweden. The emergence of this strain reinforces the necessity of infection control efforts to interrupt the spread of these organisms.

Alleles↗

PubMed2006

Examination of cfiA-mediated carbapenem resistance in Bacteroides fragilis strains from a European antibiotic susceptibility survey.

Of 1284 Bacteroides strains collected in Europe in 2000 for antibiotic susceptibility surveillance, 65 isolates displayed imipenem minimum inhibitory concentrations (MICs) > or =1 mg/L and were chosen for a thorough analysis of their resistance mechanism. Twenty-five of the isolates were positive for the cfiA carbapenem resistance gene. The resistance rates were 0.8% and 1.3% for imipenem and meropenem, respectively. In six of the strains, insertion sequence (IS) elements (IS613, IS614B, IS1186 and IS1187) activated the cfiA gene. However, other strains displayed at least elevated carbapenem MICs or were carbapenem resistant and produced measurable carbapenemase activities but did not harbour IS elements in the region upstream of the cfiA gene. The major determinant of carbapenem resistance in Bacteroides fragilis is production of CfiA metallo-beta-lactamase via activation of the cfiA gene by IS elements (higher level resistance) or by activation of its putative own promoter.

Anti-Bacterial Agents↗

PubMed2006

The challenge of the so-called electron configurations of the transition metals.

Quite different meanings are attached by chemists to the words element, atom, orbital, order of orbitals or configurations. This causes conceptual inconsistencies, in particular with respect to the transition-metal elements and their atoms or ions. The different meanings will here be distinguished carefully. They are analyzed on the basis of empirical atomic spectral data and quasi-relativistic density functional calculations. The latter are quite reliable for different average configuration energies of transition-metal atoms. The so-called "configurations of the chemical elements", traditionally displayed in periodic tables, are the dominant configurations of the lowest spin-orbit levels of the free atoms. They are chemically rather irrelevant. In many-electron systems the ns and np AOs are significantly below the more hydrogen-like nd ones. Even (n+1)s is below nd for all light neutral atoms from C onwards, but only up to the first elements of the respective long rows! The most common orbital order in transition-metal atoms is 3p << 3d < 4s etc. The chemically relevant configuration in group g is always d(g) instead of d(g-2) s(2). Conceptually clear reasoning eliminates apparent textbook inconsistencies between simple quantum-chemical models and the empirical facts. The empirically and theoretically well-founded Rydberg (n-deltal) rule is to be preferred instead of the historical Madelung (n+l) rule with its large number of exceptions.

Journal Article↗

PubMed2005

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.

BACKGROUND: The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer. RESULTS: In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism. CONCLUSION: The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Animals↗

PubMed2005

Development of a CTL vaccine for Her-2/neu using peptide-microspheres and adjuvants.

With the ultimate goal of developing a therapeutic cancer vaccine, we encapsulated the Her-2/neu peptide p369-377 in poly(lactide-co-glycolide) microspheres. This formulation was found to effectively elicit CD8+ cytotoxic T cell (CTL) responses in an HLA-A*0201 transgenic mouse model. In contrast, immunization with either peptide alone or peptide formulated in incomplete Freund's adjuvant (IFA) failed to elicit such CTL responses. Responses induced by the peptide-microsphere formulation were found to peak at approximately 6 weeks post-immunization, and were enhanced by delivering increased doses of peptide and with repeated administrations over time. Co-administration of the peptide-microspheres with adjuvants, including granulocyte-macrophage colony stimulating factor, MPL adjuvant and select synthetic Toll-Like Receptor 4 ligands, the aminoalkyl glucosaminide-4 phosphates, significantly augmented CTL responses. These studies provide important guidance for the design of human clinical trials of microsphere vaccines in terms of optimal peptide-microsphere formulation, vaccination regimen, vaccine dose, and adjuvant selection.

Adjuvants, Immunologic↗

PubMed2005

Synthesis, characteristics and biological activity of pentacoordinated spirophosphoranes derived from amino acids.

The reactions of phosphorus trichloride with various amino acids afford the pentacoordinated spirophosphoranes. The reaction procedures were traced by (31)P NMR spectra techniques. A new crystal structure of alanine derivative was characterized, which is a slightly distorted TBP structure. Besides, this kind of spirophosphoranes are potent inhibitors to tyrosinase.

Amino Acids↗

PubMed2005

Selective alterations of transcription factors in MPP+-induced neurotoxicity in PC12 cells.

MPP(+) (1-methyl-4-phenylpyridinium; the active metabolite of the neurotoxin MPTP (1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine)) depletes dopamine (DA) content and elicits cell death in PC12 cells. However, the mechanism of MPP(+)-induced neurotoxicity is still unclear. In this study, the dose response and time-course of MPP(+)-induced DA depletion and decreased cell viability were determined in nerve growth factor (NGF)-differentiated PC12 cells. The alteration of transcription factors (TFs) induced by MPP(+) from a selected dose level and time point was then evaluated using protein/DNA-binding arrays. K-means clustering analysis identified four patterns of protein/DNA-binding changes. Three of the 28 TFs identified in PC12 cells increased by 100% (p53, PRE, Smad SBE) and 2 decreased by 50% (HSE, RXR(DR1)) of control with MPP(+) treatment. In addition, three TFs decreased within the range of 33-50% (TFIID, E2F1, CREB) and two TFs increased within the range of 50-100% (PAX-5, Stat4). An electrophoretic mobility shift assay (EMSA) was used to confirm the changes of p53 and HSE. The observed changes in TFs correlated with the alterations of DA and cell viability. The data indicates that selective transcription factors are involved in MPP(+)-induced neurotoxicity and it provides mechanistic information that may be applicable to animal studies with MPTP and clinical studies of Parkinson's disease.

1-Methyl-4-phenylpyridinium↗

PubMed2005

An in silico ensemble method for lead discovery: decision forest.

Recent progress in combinatorial chemistry and parallel synthesis has radically changed the approach to drug discovery in the pharmaceutical industry. At present, thousands of compounds can be made in a short period, creating a need for fast and effective in silico methods to select the most promising lead candidates. Decision forest is a novel pattern recognition method, which combines the results of multiple distinct but comparable decision tree models to reach a consensus prediction. In this article, a decision forest model was developed using a structurally diverse training data set containing 232 compounds whose estrogen receptor binding activity was tested at the U.S. Food and Drug Administration (FDA)'s National Center for Toxicological Research (NCTR). The model was subsequently validated using a test data set of 463 compounds selected from the literature, and then applied to a large data set with 57,145 compounds as a screening example. The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery.

Decision Trees↗

PubMed2005

Removal of humic acid foulant from ultrafiltration membrane surface using photocatalytic oxidation process.

The experimental results indicated that without the TiO2 particles and PCO treatment, the permeate flux of ultrafiltration (UF) membrane declined to 40% of the initial permeate flux after 8 hours filtration. Feeding the humic acid solution with TiO2 particles dosage of 1 g/L with calcium ions into UF membrane, after the same filtration time and PCO reaction at 120 minutes, the permeate flux was increased to about 90% of the initial permeate flux. At longer PCO reaction times, a better water quality of UF permeate was observed. It has been found that with the coexistence of calcium ions in humic acid solution, the smaller molecular fragments of humic acid (HA) generated by PCO reaction may be transferred to the surface of TiO2 by means of adsorption. The humic acid adsorption by TiO2 in the presence of Ca2+ is also pH dependent. The adsorption rates were 21.0, 14.9 and 10.8 ppmTOC/gTiO2 for pH value of 4, 7 and 10 respectively. The combination of effects of PCO mineralization of humic acid into CO2 and adsorption of humic acid by TiO2 through the forming of HA-Ca(2+)-TiO2 aggregate particles were responsible for the removal of humic acid foulant from UF membrane surface.

Adsorption↗

PubMed2004

Bioavailability of butachlor and myclobutanil residues in soil to earthworms.

To establish chemical extraction procedures for predicting bioavailability of butachlor and myclobutanil in soil, several solvent systems, including methanol, methanol-water (9:1), methanol-water (1:1), acetone-water (5:3), petroleum ether and water, were assessed for their feasibility in determining extractability of the target compounds from soil samples. Experimental data showed that the extractability of butachlor and myclobutanil by the solvents was well linearly correlated with their bioavailability to Eisenia foetida and Allolobophora caliginosa, indicating that these extraction procedures may be efficient for predicting bioavailability of the two pesticides. The concentrations of the pesticides accumulated in E. foetida and A. caliginosa varied with species, suggesting that the availability of the soil-sequestered pesticide is a species-dependent process.

Acetanilides↗

PubMed2002

Dependence on initial conditions of an adsorption-desorption process.

A one-dimensional irreversible adsorption-desorption process is simulated. The critical parameters as well as the critical exponents are measured. At the critical point, the crossover between the accumulative state and the depleted state is described by a universal characteristic function.

Journal Article↗

PubMed2002

An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity.

Recent legislation mandates the US Environmental Protection Agency (EPA) to develop a screening and testing program for potential endocrine disrupting chemicals (EDCs), of which xenoestrogens figure prominently. Under the legislation, a large number of chemicals will undergo various in vitro and in vivo assays for their potential estrogenicity, as well as other hormonal activities. There is a crucial need for priority setting before this strategy can be effectively implemented. Here we report an integrated computational approach to priority setting using estrogen receptor (ER) binding as an example. This approach rationally integrates different predictive computational models into a "Four-Phase" scheme so that it can effectively identify potential estrogenic EDCs based on their predicted ER relative binding affinity (RBA). The system has been validated using an in-house ER binding assay dataset for 232 chemicals that was designed to have both broad structural diversity and a wide range of binding affinities. When applied to 58,000 chemicals identified by Walker et al. as candidates for endocrine disruption screening, some 9100 chemicals were predicted to bind to ER. Of these, only 3600 were expected to bind to ER at RBA values up to 100,000-fold less than that of 17beta-estradiol. The method ruled out 83% of the chemicals as non-binders with a very low rate of false negatives. We believe that the same integrated scheme will be equally applicable to endpoints of other endocrine disrupting mechanisms, e.g. androgen receptor binding.

Biological Assay↗

PubMed2001

Cutting edge: CCR4 mediates antigen-primed T cell binding to activated dendritic cells.

The binding of a T cell to an Ag-laden dendritic cell (DC) is a critical step of the acquired immune response. Herein, we address whether a DC-produced chemokine can induce the arrest of T cells on DC under dynamic flow conditions. Ag-primed T cells and a T cell line were observed to rapidly ( approximately 0.5 s) bind to immobilized DC at low shear stress (0.1-0.2 dynes/cm(2)) in a pertussis toxin-sensitive fashion. Quantitatively, Ag-primed T cells displayed 2- to 3-fold enhanced binding to DC compared with unprimed T cells (p < 0.01). In contrast to naive T cells, primed T cell arrest was largely inhibited by pertussis toxin, neutralization of the CC chemokine, macrophage-derived chemokine (CCL22), or by desensitization of the CCL22 receptor, CCR4. Our results demonstrate that DC-derived CCL22 induces rapid binding of activated T cells under dynamic conditions and that Ag-primed and naive T cells fundamentally differ with respect to chemokine-dependent binding to DC.

Animals↗

PubMed2001

Measurement of modulational instability gain of second-order nonlinear optical eigenmodes in a one-dimensional system.

We have investigated the amplification of a spatially periodic perturbation applied to a wide fundamental beam launched near phase matching for second-harmonic generation in a lithium niobate film waveguide. We measured the gain coefficient for the modulational instability of quadratic eigenmodes as a function of periodicity, intensity, and wave-vector mismatch. Excellent agreement with theory was obtained.

Journal Article↗

PubMed2001

Simulation of contact line dynamics in a two-dimensional capillary tube by the lattice Boltzmann model.

During immiscible-fluid displacement, the contact angle between the interface and the wall of a tube, as well as the velocity V of the contact line where a fluid interface intersects the wall of a tube, depends on the applied capillary pressure Pcap. In this paper, the contact line dynamics of immiscible-fluid displacement is simulated by using the lattice Boltzmann model in a two-dimensional capillary channel with an ideally smooth wall. The V dependence of the contact angle is studied for two different wetting cases. Our simulational results are in good agreement with those based on theoretical computations and with molecular dynamics simulations. In particular, the power-law behavior Pcap approximately Vx is found with an exponent x very close to 1. The simulations suggest that the lattice Boltzmann model may serve as an alternative reliable quantitative approach to study the contact line dynamics, and also may be a promising tool for investigating some other immiscible displacement related subjects.

Journal Article↗

PubMed2001

Frogs without polliwogs: evolution of anuran direct development.

Direct development is the assumption of the adult morphology without progression through an intervening, morphologically distinct, free-living larval phase. We discuss the ecological factors contributing to the evolution of this derived life-history strategy in frogs, and the developmental modifications that facilitate such an unusual mode of embryogenesis. Studies on the Puerto Rican tree frog, Eleutherodactylus coqui, have identified several such modifications, including developmental adaptations for dealing with increased egg size, and loss of tadpole structures. Surprisingly, this direct developer still undergoes a thyroid hormone-dependent metamorphosis, which occurs before hatching. We suggest how the ancestral biphasic developmental pattern may have been rearranged during the evolution of direct development.

Animals↗

PubMed2001

Glycerol production by microbial fermentation: a review.

Microbial production of glycerol has been known for 150 years, and glycerol was produced commercially during World War I. Glycerol production by microbial synthesis subsequently declined since it was unable to compete with chemical synthesis from petrochemical feedstocks due to the low glycerol yields and the difficulty with extraction and purification of glycerol from broth. As the cost of propylene has increased and its availability has decreased especially in developing countries and as glycerol has become an attractive feedstock for production of various chemicals, glycerol production by fermentation has become more attractive as an alternative route. Substantial overproduction of glycerol by yeast from monosaccharides can be obtained by: (1) forming a complex between acetaldehyde and bisulfite ions thereby retarding ethanol production and restoring the redox balance through glycerol synthesis; (2) growing yeast cultures at pH values near 7 or above; or (3) using osmotolerant yeasts. In recent years, significant improvements have been made in the glycerol production using osmotolerant yeasts on a commercial scale in China. The most outstanding achievements include: (1) isolation of novel osmotolerant yeast strains producing up to 130 g/L glycerol with yields up to 63% and the productivities up to 32 g/(L day); (2) glycerol yields, productivities and concentrations in broth up to 58%, 30 g/(L day) and 110-120 g/L, respectively, in an optimized aerobic fermentation process have been attained on a commercial scale; and (3) a carrier distillation technique with a glycerol distillation efficiency greater than 90% has been developed. As glycerol metabolism has become better understood in yeasts, opportunities will arise to construct novel glycerol overproducing microorganisms by metabolic engineering.

Journal Article↗

PubMed2001

Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens.

Understanding structural requirements for a chemical to exhibit estrogen receptor (ER) binding has been important in various fields. This knowledge has been directly and indirectly applied to design drugs for human estrogen replacement therapy, and to identify estrogenic endocrine disruptors. This paper reports structure-activity relationships (SARs) based on a total of 230 chemicals, including both natural and xenoestrogens. Activities were generated using a validated ER competitive binding assay, which covers a 10(6)-fold range. This study is focused on identification of structural commonalities among diverse ER ligands. It provides an overall picture of how xenoestrogens structurally resemble endogenous 17beta-estradiol (E(2)) and the synthetic estrogen diethylstilbestrol (DES). On the basis of SAR analysis, five distinguishing criteria were found to be essential for xenoestrogen activity, using E(2) as a template: (1) H-bonding ability of the phenolic ring mimicking the 3-OH, (2) H-bond donor mimicking the17beta-OH and O-O distance between 3- and 17beta-OH, (3) precise steric hydrophobic centers mimicking steric 7alpha- and 11beta-substituents, (4) hydrophobicity, and (5) a ring structure. The 3-position H-bonding ability of phenols is a significant requirement for ER binding. This contributes as both a H-bond donor and acceptor, although predominantly as a donor. However, the 17beta-OH contributes as a H-bond donor only. The precise space (the size and orientation) of steric hydrophobic bulk groups is as important as a 17beta-OH. Where a direct comparison can be made, strong estrogens tend to be more hydrophobic. A rigid ring structure favors ER binding. The knowledge derived from this study is rationalized into a set of hierarchical rules that will be useful in guidance for identification of potential estrogens.

Animals↗