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Biomedical subjects

J Qi

Publications and source records attributed to J Qi.

At least 19 recordsLinked to original sources
PubMed2006

Archaea predominate among ammonia-oxidizing prokaryotes in soils.

Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.

Ammonia↗
PubMed2006

Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment.

MOTIVATION: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species. RESULT: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes. AVAILABILITY: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi.pku.edu.cn.

Algorithms↗
PubMed2006

Measurement of the electronic transition dipole moment by Autler-Townes splitting: Comparison of three- and four-level excitation schemes for the Na2 A 1Sigma(u)+ - X 1Sigma(g)+ system.

We present a fundamentally new approach for measuring the transition dipole moment of molecular transitions, which combines the benefits of quantum interference effects, such as the Autler-Townes splitting, with the familiar R-centroid approximation. This method is superior to other experimental methods for determining the absolute value of the R-dependent electronic transition dipole moment function mu(e)(R), since it requires only an accurate measurement of the coupling laser electric field amplitude and the determination of the Rabi frequency from an Autler-Townes split fluorescence spectral line. We illustrate this method by measuring the transition dipole moment matrix element for the Na2 A 1Sigma(u)+ (v' = 25, J' = 20e)-X 1Sigma(g)+ (v" = 38, J" = 21e) rovibronic transition and compare our experimental results with our ab initio calculations. We have compared the three-level (cascade) and four-level (extended Lambda) excitation schemes and found that the latter is preferable in this case for two reasons. First, this excitation scheme takes advantage of the fact that the coupling field lower level is outside the thermal population range. As a result vibrational levels with larger wave function amplitudes at the outer turning point of vibration lead to larger transition dipole moment matrix elements and Rabi frequencies than those accessible from the equilibrium internuclear distance of the thermal population distribution. Second, the coupling laser can be "tuned" to different rovibronic transitions in order to determine the internuclear distance dependence of the electronic transition dipole moment function in the region of the R-centroid of each coupling laser transition. Thus the internuclear distance dependence of the transition moment function mu(e)(R) can be determined at several very different values of the R centroid. The measured transition dipole moment matrix element for the Na2 A 1Sigma(u)+ (v' = 25, J' = 20e)-X 1Sigma(g)+ (v" = 38, J" = 21e) transition is 5.5+/-0.2 D compared to our ab initio value of 5.9 D. By using the R-centroid approximation for this transition the corresponding experimental electronic transition dipole moment is 9.72 D at Rc = 4.81 A, in good agreement with our ab initio value of 10.55 D.

Journal Article↗
PubMed2006

Imaging of primary adrenal lymphoma: case report and literature review.

Primary adrenal lymphoma is very rare, and correct preoperative diagnosis is difficult because of its nonspecific imaging findings. We report a case of bilateral primary adrenal lymphoma, with the largest dimension of 18 cm, which is the largest one reported so far, to our knowledge. Computed tomography (CT) and magnetic resonance (MR) findings were not specific enough to establish a correct diagnosis, but positron emission tomography/CT (PET/CT) showed high fluorodeoxyglucose (FDG) uptake, indicating its malignant nature. We describe the imaging findings and review the related literature to highlight this uncommon entity.

Adrenal Gland Neoplasms↗
PubMed2004

Photoassociative production and trapping of ultracold KRb molecules.

We have produced ultracold heteronuclear KRb molecules by the process of photoassociation in a two-species magneto-optical trap. Following decay of the photoassociated KRb*, the molecules are detected using two-photon ionization and time-of-flight mass spectroscopy of KRb+. A portion of the metastable triplet molecules thus formed are magnetically trapped. Photoassociative spectra down to 91 cm(-1) below the K(4s)+Rb(5p(1/2)) asymptote have been obtained. We have made assignments to all eight of the attractive Hund's case (c) KRb* potential curves in this spectral region.

Journal Article↗
PubMed2004

Functional expression of ATM gene carried by HSV amplicon vector in vitro and in vivo.

Ataxia-telangiectasia (AT) is a human autosomal recessive disease with a pleiotropic phenotype characterized by cerebellar degeneration, immunodeficiency, premature aging, cancer predisposition, and radiation sensitivity. The gene mutated in AT, ATM (for AT-mutated), had been cloned and found to have ionizing radiation and oxidative stress-inducible kinase activity. No treatment can stop the progression of the disease. In this study, the complete open-reading frame of ATM cDNA was cloned into a Herpes simplex virus type-1 (HSV-1) amplicon vector (pTO-ATM), and the transduction of cultured AT cells was demonstrated by immunohistochemistry and Western blot analysis. Functional gene expression was evaluated by cell colony-forming assays following exposure to oxidative stress. The survival of AT cells with ATM gene transduction was about 100% higher compared to nontransduced cells after t-butyl hydroperoxide treatments. Next, the normal ATM gene expression in different regions of the rat brain was studied. Immunohistochemistry staining demonstrated weak endogenous ATM protein expression in neurons of the caudate-putamen, with significantly higher levels of expression detected in neurons in other brain regions. Exogenous ATM gene expression from pTO-ATM after viral transduction in the caudate-putamen of the adult rat was examined. At 3 days after injection of the pTO-ATM viral vector, abundant positive ATM staining of the neurons was found at the injection sites, in comparison to the controls. These data demonstrate that the relatively large ATM cDNA can be transduced and expressed in vitro and in vivo from an HSV amplicon viral vector. These data provide initial evidence that the replacement of the ATM gene into the cells of AT patients might be possible some day.

Animals↗
PubMed2003

Total-internal-reflection mode in holographic polymer dispersed liquid crystals.

We have developed a holographic polymer dispersed liquid-crystal device based on total internal reflection (TIR). In the field-off state, the holographic planes are slanted such that the angle of the diffraction beam is beyond the TIR angle of the glass substrate. The beam is trapped in the sample and propagates to the edge. In the field-on state, the holographic grating is erased and the incident beam propagates directly through the sample. Contrast ratios of 10 dB, submillisecond response times, and an index modulation of 0.042 at 1550 nm are reported.

Journal Article↗
PubMed2003

Tunable face-centered-cubic photonic crystal formed in holographic polymer dispersed liquid crystals.

We report on the fabrication and electro-optic measurements of face-centered-cubic (fcc) lattices in holographic polymer dispersed liquid-crystal materials. Four linearly polarized coherent plane waves were interfered to generate a fcc optical lattice that was subsequently and indefinitely recorded as an arrayed pattern of nanometer-sized liquid-crystal droplets (approximately 50 nm) at lattice nodes within a polymer matrix. Observed transmission spectra and Kossel diffraction curves are consistent with fcc crystal structure. A completely reversible 2% wavelength shift of the (+/- 111) stop band was observed on application of an electric field.

Journal Article↗
PubMed2003

Immobilized MICA could expand human Vdelta1 gammadelta T cells in vitro that displayed major histocompatibility complex class I chain-related A-dependent cytotoxicity to human epithelial carcinomas.

Human major histocompatibility complex class I chain-related A (MICA) is a human leucocyte antigen-related polymorphic molecule, which is expressed on many kinds of epithelial tumours and can be recognized by the Vdelta1 subset of gammadelta T cells. In the present study, monoclonal antibodies (MoAbs) were produced in mice immunized with recombinant MICA (rMICA)*008. It was found that MICA was expressed on ovarian and colonic tumour tissues and could be detected by these anti-MICA MoAbs. The immobilized rMICA could induce the proliferation of human ovarian epithelial carcinoma- or colonic carcinoma-derived gammadelta T cells of the Vdelta1 phenotype in vitro. These Vdelta1 T cells displayed a strong, broad-range cytolytic activity towards tumour cell lines positive for MICA. The efficiency of this cytolytic activity depended greatly on the level of MICA expressed on the cell surface and could be inhibited by anti-MICA MoAbs. Therefore, MICA may play an important role in immune responses against epithelial tumours and function as a stimulating factor for the growth of Vdelta1 gammadelta T cells, whereas MICA-reactive Vdelta1 gammadelta T cells might serve as a new candidate for adoptive cellular therapy of tumours.

Adult↗
PubMed2002

Internet2-based 3D PET image reconstruction using a PC cluster.

We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

Algorithms↗
PubMed2002

Chemical profile of two types of oral snuff tobacco.

The chemical-analytical profile of two US brands of oral moist snuff was determined. These two brands were bought in five geographical locations (NY, MA, CO, CA and KY in the US). They were mixed thoroughly to yield representative samples. Brand A had a pH of 5.84 and nicotine content of 0.42%, while brand B had a pH of 7.99 and nicotine content of 2.73%. At pH 5.84, only 1% of the nicotine is present as a free base while 59% of nicotine is present in unprotonated form at pH 7.99. It is the unprotonated form of nicotine that is most readily absorbed through the mucous membrane in the oral cavity. Snuff A contained also significantly lower levels of moisture, nitrate, nitrite and tobacco-specific nitrosamines than snuff B. The University of Kentucky reference snuff 1S3 was analyzed as an external control sample. These two snuff brands are currently being assayed with rats in a short-term and in long-term bioassays to test the concept that the tobacco-specific N-nitrosamines are major contributors to the carcinogenic activity of oral snuff.

Hydrogen-Ion Concentration↗
PubMed2001

Role of snare proteins in CFTR and ENaC trafficking.

The apical membrane ion channels, CFTR and ENaC, undergo regulated trafficking as a means of controlling their plasma membrane density. This provides a mechanism for regulating the Cl and Na conductance properties of epithelial apical membranes, and thus the transepithelial ion transport rates. Physical and functional interactions between these channels and SNARE proteins, in particular syntaxin 1A (S1A), provide a mechanism for linking the known vesicle fusion machinery with this process. In this paper we summarize evidence indicating that the interaction of S1A with CFTR and ENaC reduces channel currents in a syntaxin-isoform-specific manner. The acute cAMP-regulated CFTR trafficking event, which is reported by an increase in membrane capacitance in response to cAMP, is also inhibited by exogenous S1A expression. We tagged both channels with flag epitopes on their extracellular surfaces to monitor their plasma membrane expression as a function of S1A co-expression. The data indicate that the reduction in current caused by S1A is associated with a marked decrease in the amount of CFTR or ENaC detected at the cell surface. These findings suggest that S1A inhibits ion channel insertion into the plasma membrane, either by disrupting the stoichiometry of SNARE protein associations that mediate channel trafficking, or by physically associating with the channels to prevent their insertion. These data link the SNARE machinery to the regulation of apical membrane ion channel density, and suggest that phosphorylation-dependent interactions of these channels with SNARE proteins may acutely regulate this process.

Cystic Fibrosis↗
PubMed2001

Chloroplast glyceraldehyde-3-phosphate dehydrogenase contains a single disulfide bond located in the C-terminal extension to the B subunit.

Mass mapping analysis based on cyanylation and CN-induced cleavage indicates that the two cysteine residues in the C-terminal extension of the B subunit of the light-activated pea leaf chloroplast glyceraldehyde-3-phosphate dehydrogenase form a disulfide bond. No evidence was found for a disulfide bond in the A subunit, nor was there any indication of a second disulfide bond in the B subunit. The availability of the structure of the extended glyceraldehyde-3-phosphate dehydrogenase from the archaeon Sulfolobus solfataricus allows modeling of the B subunit. As modeled, the two cysteine residues in the extension are positioned to form an interdomain disulfide cross-link.

Amino Acid Sequence↗
PubMed2001

Determination of the disulfide structure of sillucin, a highly knotted, cysteine-rich peptide, by cyanylation/cleavage mass mapping.

The disulfide structure of sillucin, a highly knotted, cysteine-rich, antimicrobial peptide, isolated from Rhizomucor pusillus, has been determined to be Cys2--Cys7, Cys12--Cys24, Cys13--Cys30, and Cys14--Cys21 by disulfide mass mapping based on partial reduction and CN-induced cleavage enabled by cyanylation. The denatured 30-residue peptide was subjected to partial reduction by tris(2-carboxyethyl)phosphine hydrochloride at pH 3 to produce a mixture of partially reduced sillucin species; the nascent sulfhydryl groups were immediately cyanylated by 1-cyano-4-(dimethylamino)pyridinium tetrafluoroborate. The cyanylated species, separated and collected during reversed phase high-performance liquid chromatography, were treated with aqueous ammonia, which cleaved the peptide chain on the N-terminal side of cyanylated cysteine residues. The CN-induced cleavage mixture was analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry before and after complete reduction of residual disulfide bonds in partially reduced and cyanylated species to mass map the truncated peptides to the sequence. Because the masses of the CN-induced cleavage fragments of both singly and doubly reduced and cyanylated sillucin are related to the linkages of the disulfide bonds in the original molecule, the presence of certain truncated peptide(s) can be used to positively identify the linkage of a specific disulfide bond or exclude the presence of other possible linkages.

Amino Acid Sequence↗