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.

Measurement of the electronic transition dipole moment by Autler-Townes splitting: Comparison of three- and four-level excitation schemes for the Na2AΣu+1−XΣg+1 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.

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.

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.

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.

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.

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.

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.

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.

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.

Measurement of transition dipole moments in lithium dimers using electromagnetically induced transparency

We have observed electromagnetically induced transparency in a Doppler broadened molecular cascade system using fluorescence detection. We demonstrate that the power-dependent splitting of lines in the upper-level fluorescence excitation spectrum can be used as a new spectroscopic tool for the measurement of molecular transition dipole moment functions.

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.

Fine needle aspiration cytology diagnosis of renal medullary carcinoma: a case report

BACKGROUND

Renal medullary carcinoma is a recently described, highly aggressive neoplasm that affects predominantly young African American males with a history of sickle cell trait. To the best of our knowledge, this is the first report of fine needle aspirate cytology (FNAC) findings of renal medullary carcinoma.

CASE

A 14-year-old, African American male with a history of sickle cell trait presented with the sudden onset of third cranial nerve palsy. Radiographic examination demonstrated possible tumor masses in the brain, thorax and left kidney. Ultrasound-guided fine needle aspiration was performed on the left kidney, and a cytologic diagnosis of "suspect renal medullary carcinoma" was rendered. The cytologic diagnosis was confirmed by tissue examination.

CONCLUSION

The cytologic features of renal medullary carcinoma include loosely cohesive clusters and single epithelioid cells with cytologic atypia, including high nuclear/cytoplasmic ratios, hyperchromasia, prominent nucleoli and cytoplasmic vacuolation. These cytologic findings, coupled with clinical findings (young black male with sickle cell trait), allow recognition of this rare renal neoplasm.

Alleviation of hypoxic pulmonary vascular structural remodeling by L-arginine

OBJECTIVE

To explore the effect of L-arginine on hypoxic pulmonary vascular structural remodeling and its possible mechanisms.

METHODS

Eighteen Wistar rats were randomly divided into three groups: the hypoxia group, the hypoxia with L-arginine group and the control group. Pulmonary artery mean pressure was evaluated with right cardiac catheterization. Pulmonary vascular structural changes were also observed. Plasma concentration of nitric oxide (NO) was measured via spectrophotometry, and endothelin-1 (ET-1) mRNA expression in pulmonary artery endothelial cells was detected using in situ hybridization.

RESULTS

The pulmonary artery mean pressure was significantly high in hypoxic rats than in normal controls (20.33 +/- 2.18 mm Hg vs 15.38 +/- 1.05 mm Hg, P < 0.05). Microstructural and ultrastructural analysis revealed the development of hypoxic pulmonary vascular structural remodeling in the hypoxic rats. Meanwhile, the plasma NO concentration was markedly lower in the hypoxic rats than in controls (P < 0.05). The expression signals of ET-1 mRNA by pulmonary artery endothelial cells of hypoxic rats strengthened obviously. L-arginine ameliorated pulmonary hypertension (16.73 +/- 1.35 mm Hg vs 20.33 +/- 2.18 mm Hg, P < 0.05) as well as pulmonary vascular structural remodeling in the hypoxic rats in association with an increase in plasma NO concentration (P < 0.05) and inhibited ET-1 mRNA expression by the endothelial cells of pulmonary arteries.

CONCLUSION

L-arginine might play an important role in the regulation of hypoxic pulmonary vascular structural remodeling and hypoxic pulmonary hypertension. The mechanism is probably related to promoting NO production and, as a result, inhibiting ET-1 mRNA expression by pulmonary artery endothelial cells in hypoxic rats.

[The predomination of rotavirus G3 serotype among children with diarrhea in Lulong County in 1998]

OBJECTIVE

To investigate the epidemiology of rotavirus diarrhea among children in rural population.

METHODS

120 stool specimens collected from children with diarrhea during the winter of 1998 in Lulong County, Hebei Province were examined for rotavirus by PAGE and ELISA and for serotype by ELISA and PCR.

RESULTS

Rotavirus was detected in children aged between 2-24 months. The positive rate of rotavirus was 39.2% and the ratio of male to female was 1-1.47. All rotavirus RNA profiles were long pattern. The distribution of rotavirus serotypes was type 3(61.7%), followed by type 1(36.2%), and type 4(6.4%).

CONCLUSIONS

The epidemiology of rotavirus diarrhea during 1998 rotavirus season in Lulong County was similar to that of other regions in China, but rotavirus serotype G3 was a prevalent strain in Lulong County, which was uncommon and different from the predominant G1 in other places throughout China.

[Simulation study of electrode configurations for cardiac stroke volume calculation by 3-dimensional finite element method]

This is a research in Kubicek electrode configurations for cardiac stroke volume calculation from the angle of Kubicek model simulation by 3-dimensional finite element method. In the process of computer simulation, we have studied, respectively, the effect of the width, thickness, and material property (specific resistance) of potential electrode band on cardiac stroke volume calculation in order to guide the choice of electrode configurations in the clinic. The simulation results showed that in Kubicek electrode configurations, its all properties of the potential electrode band affected the impedance results for cardiac stroke volume calculation, one main factor of which is the choice of the material property. Therefore, we have to attend to the choice of Kubicek electrode configurations while calculating SV by Kubicek method in order to improve the accuracy of SV calculation.

[Degradation of nitrobenzene in water by electrohydrodynamic DC discharge]

In this paper, the experimental results with respect to the degradation of nitrobenzene in water using electrohydrodynamic DC discharge were presented. The DC voltage was 40 kV, the degradation efficiency in the first discharge process reached 50%, the total degradation efficiency in the second discharge process reached 80%. The products contained acetone. At the same time, the degradation efficiency variation with the voltage polarity, flux, and concentration were studied. These studies will be helpful to the treatment of organic wastewater.

Neuritogenic cerebrosides from an edible Chinese mushroom. Part 2: Structures of two additional termitomycesphins and activity enhancement of an inactive cerebroside by hydroxylation

Termitomycesphins E and F, novel cerebrosides that are hydroxylated around the middle of the long-chain base (LCB), have been isolated from the edible Chinese mushroom Termitomyces albuminosus (Berk.) Heim. ('Jizong' in Chinese) together with termitomycesphins A-D, and shown to induce neuronal differentiation in rat PC12 cells. Their stereostructures have been determined based on their chemical derivatization and spectroscopic analysis. The major cerebroside obtained from the same mushroom was not hydroxylated around the middle of the LCB and was inactive against PC12 cells, suggesting the importance of the extra hydroxyl group on LCB. The Di- and tetrahydroxylation of this inactive cerebroside resulted in the enhancement of its neuritogenic activity.

Theoretical study of lesion detectability of MAP reconstruction using computer observers

The low signal-to-noise ratio (SNR) in emission data has stimulated the development of statistical image reconstruction methods based on the maximum a posteriori (MAP) principle. Experimental examples have shown that statistical methods improve image quality compared to the conventional filtered backprojection (FBP) method. However, these results depend on isolated data sets. Here we study the lesion detectability of MAP reconstruction theoretically, using computer observers. These theoretical results can be applied to different object structures. They show that for a quadratic smoothing prior, the lesion detectability using the prewhitening observer is independent of the smoothing parameter and the neighborhood of the prior, while the nonprewhitening observer exhibits an optimum smoothing point. We also compare the results to those of FBP reconstruction. The comparison shows that for ideal positron emission tomography (PET) systems (where data are true line integrals of the tracer distribution) the MAP reconstruction has a higher SNR for lesion detection than FBP reconstruction due to the modeling of the Poisson noise. For realistic systems, MAP reconstruction further benefits from accurately modeling the physical photon detection process in PET.

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.

Prediction of programmed-temperature retention values of naphthas by wavelet neural networks

The wavelet neural network (WNN) was used to predict the programmed-temperature retention values of naphthas. In WNN, a Morlet mother wavelet was used as a transfer function, and the convergence speed was faster than other neural networks. Sixty-four compounds (selected randomly from 94) were used as a training set, and the 30 remaining compounds were used as a test set. A very satisfactory result was obtained only after about 8000 training epochs. The other two methods, the artificial neural network (ANN) and the Simpson integral method, were also used for this study. The comparison of results obtained from three methods showed that the WNN is the most suitable tool in predicting programmed-temperature retention values of naphthas, consequently this method can be used to provide reliable data for the petrochemical industry.