A weighting method for predicting protein structural class from amino acid composition

A protein is generally classified into one of the following four structural classes: all alpha, all beta, alpha+beta and alpha/beta. In this paper, based on the weighting to the 20 constituent amino acids, a new method is proposed for predicting the structural class of a protein according to its amino acid composition. The 20 weighting parameters, which reflect the different properties of the 20 constituent amino acids, have been obtained from a training set of proteins through the linear-programming approach. The rate of correct prediction for a training set of proteins by means of the new method was 100%, whereas the highest rate of previous methods was 82.8%. Furthermore, the results showed that the more numerous training proteins, the more effective the new method.

Ablation of transplanted HTLV-I Tax-transformed tumors in mice by antisense inhibition of NF-kappa B

Mice transgenic for the human T cell leukemia virus (HTLV-I) Tax gene develop fibroblastic tumors that express NF-kappa B-inducible early genes. In vitro inhibition of NF-kappa B expression by antisense oligodeoxynucleotides (ODNs) inhibited growth of these culture-adapted Tax-transformed fibroblasts as well as an HTLV-I-transformed human lymphocyte line. In contrast, antisense inhibition of Tax itself had no apparent effect on cell growth. Mice treated with antisense to NF-kappa B ODNs showed rapid regression of transplanted fibrosarcomas. This suggests that NF-kappa B expression may be necessary for the maintenance of the malignant phenotype and provides a therapeutic approach for HTLV-I-associated disease.

[The possible role of sperm in family HBV infection]

The paper investigated HBV infectious markers in the sperm and spermatozoa of 31 male patients with hepatitis B, in the serum of their 31 spouses and 35 children respectively. HBV markers were found in 12 sperm samples, HBV-DNA was detected in 6 samples of spermatozoa (3 integrated forms and 3 free forms). The samples were hybridized repeatedly with probes of 82P labeled HBV-DNA 82P labeled lambda DNA and 82P labeled pBR822 to exclude false-positive possibility. 8 out of 12 wives (66.67%), were infected whose husband's sperm reacted positively with HBV 8 out of 14 children were infected (57.14%), whose father's sperm had HBV markers, 6 women out of 19 were infected (31.58%) whose husband's sperm did not react with HBV, 11 of 22 children were infected (50%). The investigation found that the HBV in sperm was higher in the patients with HBeAg positive serum. The wives were easier infected from husbands with HBV positive sperm. The result suggested that sperm must be one of medium of HBV transmission. HBsAg HBeAg anti-HBc HBV-DNA were found in the serum sample of one 4 month infant, with no anti-HBc-IgM. His mother was negative in HBV. The integrated form HBV-DNA was detected in his father's spermatozoa. The transmission between father and son is perhaps mainly by contact each other daily. If HBV has the possibility of vertical transmission is to be studied.

Effects of cigarette smoking on rate of loss of pulmonary function in adults: a longitudinal assessment

Data from a random sample of 8,191 men and women selected in six U.S. cities and examined on three occasions over a 6-yr follow-up period were analyzed by longitudinal methods to describe the effects of smoking history and current smoking behavior on rate of loss of pulmonary function during adult life. Former smokers had age- and height-adjusted rates of decline (34.3 ml/yr for men and 29.6 ml/yr for women) comparable with those of never smokers (37.8 ml/yr for men and 29.0 ml/yr for women) but much smaller than those of continuing smokers (52.9 ml/yr for men and 38.0 ml/yr for women). The accelerated rate of loss of FEV1 among smokers depended linearly on the number of cigarettes smoked per day during the interval between examinations. The estimated increase in rate of loss associated with smoking was 12.6 ml/yr per pack/day for men and 7.2 ml/yr per pack/day for women. These longitudinal estimates of the effects of smoking were approximately 50% larger than estimates obtained from cross-sectional analysis of the initial pulmonary function examination. Men who started smoking had accelerated rates of loss (55.9 ml/yr) as did women (43.1 ml/yr). Smokers who stopped smoking between examinations had reduced declines (41.2 ml/yr for men and 28.7 ml/yr for women) compared with continuing smokers. The age-specific rates of loss suggest that the benefits of cessation may be greatest among the youngest smokers.(ABSTRACT TRUNCATED AT 250 WORDS)

Infrared Reflection-Absorption Spectroscopy and STM Studies of Model Silica-Supported Copper Catalysts

The structure of model silica-supported copper catalysts has been investigated with scanning tunneling microscopy (STM) and infrared reflection-absorption spectroscopy (IRAS). The IRAS studies of CO on the model silica-supported copper catalysts indicate that there are several types of copper clusters with surface structures similar to (111), (110), and other high-index planes of single-crystal copper. The STM studies show several types of copper clusters on silica and reveal images of metal clusters on an amorphous oxide support with atomic resolution.

Filling in of Fraunhofer lines in the ocean by Raman scattering

We have developed a Monte Carlo program that can account for Raman scattering in the ocean when polarization effects are not considered. The program is capable of coupling an inhomogeneous atmosphere to an inhomogeneous ocean through a dielectric interface. We have studied the filling in of both the 486-nm H(beta) and the 518-nm Mg Fraunhofer lines caused by Raman scattering in the ocean. The amount of fill varies with solar zenith angle, angle of view, depth in the ocean, and magnitude of the cross sections. By monitoring the shapes of Fraunhofer lines we can learn a great deal about the relative importance of this inelastic process in oceanic optics.

Longitudinal lung function decline in subjects with respiratory symptoms

The relation of respiratory symptoms and lung function has not been extensively investigated. To determine better the rate of FEV1 decline in subjects reporting persistent wheeze, chronic cough, chronic phlegm, and/or dyspnea, longitudinal data from an adult population sample of 3,948 subjects (1,757 men; 2,191 women) followed for 12 yr were analyzed. At the initial and subsequent follow-up visits, subjects completed a standardized respiratory questionnaire and performed spirometry using the same methods and spirometers. Subjects were categorized based on the presence or absence of self-reported respiratory symptoms (persistent wheeze, chronic cough, chronic phlegm, or shortness of breath) at the initial visit. Six-specific linear regression models were fitted to determine the effect of these respiratory symptoms on lung function. In both men and women, reporting of any respiratory symptoms was associated with both a reduction in initial lung function and more rapid decline in height-adjusted FEV1. Furthermore, after adjustment for height, age, and cigarette smoking, men with cough or phlegm and women with cough alone showed accelerated loss in FEV1. Clinicians should be aware of the predictive value of these respiratory symptoms, because therapeutic intervention may modify the associated decline in lung function.

Immunity to Hantavirus Challenge in Meriones Unguiculatus Induced by Vaccinia-Vectored Viral Proteins

Vaccinia virus recombinants were constructed that incorporated genomic sequences coding for the nucleoprotein (N) and glycoproteins (G1 and G2) of the hantavirus R22 strain isolated from a rat in China, and designated as RNV and RMV9, respectively. The proteins expressed by RNV and RMV9 were identified by radioimmunoprecipitation and indirect immunofluorescence assay using a panel of monoclonal antibodies and polyclonal immune sera, and were found to be antigenically indistinguishable from authentic R22 viral proteins. Both RNV and RMV9 elicited an anti-R22 antibody response in Mongolian gerbils (Meriones unguiculatus) with titers ranging from 6,400 to 12,800 by enzyme-linked immunosorbent assay, but only RMV9 produced neutralizing antibodies to R22 virus (titer 1:200) and Hantaan (HTN) virus (titer 1:20). The ability of these recombinants to protect Mongolian gerbils against challenge with R22 and HTN viruses was examined. The RMV9 recombinant induced a complete protective immune response against challenge with 10(4) plaque-forming units (PFU) of both R22 and HTN viruses, while RNV induced partial protection against a challenge with the homologous R22 virus and the heterologous HTN virus at a dose of 10(3) PFU. Our data show that the common antigenic sites responsible for eliciting a protective response are located mainly on hantavirus glycoproteins, and that the nucleoprotein may also confer partial cross-protection that presumably involves cell-mediated as well as humoral mechanisms.

Host range analysis of a chimeric simian virus 40 genome containing the BKV capsid genes

Simian virus 40 (SV40) propagates poorly in cells from human embryonic kidney (HEK) and human fetal fibroblasts (HFF) while BK virus grows well in many human cell types. It has been suggested that sequences within the SV40 late region but not within the BKV late region may act to inhibit growth of virus in HEK and HFF cells. In order to test this and to identify a late region host range function, we have replaced the late region of wtSV40 DNA with the late region of RFV (a variant of BKV) to produce an intermolecular hybrid or chimera. The constructed SV40/RFV chimeric genome contained approx. 5900 base pairs, more than 650 base pairs greater than wtSV40. Nevertheless, when introduced by transfection the chimera appeared to be infectious. Three chimeric genomes were recovered from infected cells and all contained deletions of nearly 600 base pairs, exclusively at the region of the 3' terminal junction. Since all three chimeras propagated in human HFF and HEK cells, the RFV late region and not the RFV regulatory region possesses a host range function required for growth in human cells. Analysis of T-antigen gene expression suggests that the replacement of the SV40 late region with the BKV late region leads to full expression of the SV40 early region in human cells. Two chimeras exhibited a BKV-like host range and the third exhibited both a BKV and an SV40-like host range. We determined precisely which sequences were deleted in each chimera and we exchanged 3' terminal junction fragments containing these deletions, between two chimeras with different host ranges. From these experiments we demonstrated that: (1) The 3' terminus of the SV40 large T-antigen gene is required for growth of SV40/RFV in TC-7 and CV-1 simian cells but not for growth in human cells; (2) while the SV40 late region is refractory for growth in human cells, the RFV late region is not refractory for growth in simian cells; (3) the 3' terminus of the RFV T-antigen gene is not required for growth in human cells. The results of the 3' terminal junction exchanges and studies of early gene expression also demonstrate that BKV and SV40 can penetrate human and simian cells, even when they failed to grow in one cell type.

Optical adder that uses spatial light rebroadcasters

We show novel experimental results for an all-optical cascadable module that consists of a spatial light rebroadcasters, an image intensifier, and a liquid-crystal light valve. The module may be used for all-optical logic, memory, or arithmetic. Previous experimental systems involving spatial light rebroadcasters use a video camera and computer to overcome their lack of cascadability. The results of laboratory experiments show correct operation for a half-adder constructed from the cascadable module. Optical setups are proposed for constructing all-optical parallel ripple-carry and bit-slice full adders by using a single optical half-adder.

[Bacterial microcolony and its primary applications]

A new rapid and useful microcolony technique was developed by using cellulose-acetate membrane as a supporter. The bacteria were inoculated on the membrane and cultivated for 3-6h. Then the membrane was rendered, fixed and colored. The microcolonies were observed and counted under the microscope. By using this technique the microcolonies of 139 strains of bacteria were observed. 72 strains of Staphylococcus were differentiated by means of observing the characteristics of the microcolonies. The correlation rate between the microcolony method and the routine method was 90.28%. This technique was also first used to determine the bacteria numbers in urine within 6h, and the advantages of it were significant compared with the plate count method.

The importance of aspartate 327 for catalysis and zinc binding in Escherichia coli alkaline phosphatase

In order to investigate the function of Asp-327, a bidentate ligand of one of the zinc atoms in Escherichia coli alkaline phosphatase, and the importance of this zinc atom in catalysis, site-specific mutagenesis was used to convert Asp-327 to either asparagine or alanine. The 10(7)-fold decrease in the kcat/Km ratio observed for the Asp-327----Ala enzyme compared to the wild-type enzyme indicates that the side chain of Asp-327 is important for zinc binding at the M1 site. However, only one of the two carboxyl oxygens of Asp-327 is essential for zinc binding, since the Asp-327----Asn enzyme shows approximately the same hydrolysis activity as the wild-type enzyme. The fact that the enzymatic activity of this mutant enzyme shows a dependence on zinc concentration suggests that the other carboxyl oxygen or the negative charge on the side chain of Asp-327 is important in binding of the zinc at the M1 site. However, the zinc hydroxyl must still be appropriately positioned to attack the phosphoserine in the Asp-327----Asn enzyme; therefore, the negative charge and at least one carboxyl oxygen of the side chain are not directly involved in positioning or deprotonating the zinc hydroxyl. 31P NMR studies indicate that the Asp-327----Asn enzyme exhibits transphosphorylation activity at both pH 8.0 and pH 10.0, but at a reduced level compared to the wild-type enzyme. The biphasic production of 2,4-dinitrophenylate in the pre-steady-state kinetics of the mutant enzymes at pH 5.5 suggests that the breaking of the phosphoenzyme covalent complex is rate-limiting for both mutant enzymes. These results suggest that the main function of the zinc atom at the M1 site in catalysis involves decomposition of the phosphoenzyme covalent complex and that it may be important in helping to stabilize the alcohol leaving group.

Gene cluster of the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans: characterization of four structural gene products

In previous reports from our laboratory, the three structural genes (NQO1, NQO2, and NQO3) of the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans were characterized [Xu, X., Matsuno-Yagi, A., & Yagi, T. (1991) Biochemistry 30, 6422-6428; (1991) Biochemistry 30, 8678-8684; (1992) Arch. Biochem. Biophys. 296, 40-48]. In this report, the four structural genes NQO4, NQO5, NQO6, and NQO7 of the same Paracoccus denitrificans oxidoreductase were cloned and sequenced. On the basis of sequence homology and immunological cross-reactivity, these genes encode counterparts of the 49-, 30-, and 20-kDa polypeptides and the mitochondrial DNA ND3 polypeptides of bovine mitochondrial complex I. These seven structural genes were found to be located in the same gene cluster. The order of the seven structural genes of the Paracoccus NADH-quinone oxidoreductase in the gene cluster is NQO7, NQO6, NQO5, NQO4, NQO2, NQO1, and NQO3. Upstream of the NQO7 gene, an open reading frame encoding a predicted polypeptide homologous to the UV repair enzyme A of Escherichia coli and Micrococcus lysodeikticus was detected. The 5'-terminus of the gene cluster carrying the Paracoccus NADH-quinone oxidoreductase was studied, and the possible promoter region is discussed. The NQO4 and NQO5 genes appear to code for the M(r) 48,000 and 21,000 polypeptides of the isolated Paracoccus NADH dehydrogenase complex [Yagi, T. (1986) Arch. Biochem. Biophys. 250, 302-311] on the basis of amino acid analyses and N-terminal protein sequence analyses. The antisera to the bovine complex I 49- and 30-kDa polypeptides cross-reacted with the Paracoccus 48- and 21-kDa subunits, respectively.

Exposure-response relationships between occupational exposures and chronic respiratory illness: a community-based study

Data from a random sample of 3,606 adults 40 to 69 yr of age residing in Beijing, China, were analyzed to investigate the association of reported occupational exposures to dusts and gases/fumes with the prevalence of chronic respiratory symptoms and level of pulmonary function. The prevalence of occupational dust exposure was 32%, and gas or fume exposure, 19%. After we adjusted for age, sex, area of residence, smoking status, coal stove heating, and education, an increased prevalence of chronic phlegm and breathlessness was significantly related to both types of exposures. Chronic cough was significantly related only to dust exposure, and persistent wheeze only to fume exposure. The global estimates of the relative odds of the four symptoms were 1.30 (95% CI [confidence interval] 1.09 to 1.48) and 1.27 (95% CI 1.09 to 1.48), respectively, for dusts and for gases/fumes. These two occupational exposures are associated with chronic respiratory symptoms independent of smoking, gender, and each other. There was an increasing prevalence of each symptom with increasing dust and fume exposure, represented by the index of cumulative exposure duration and exposure intensity. Linear trends for increased prevalence of chronic bronchitis and breathlessness were significant for both exposures, while the linear trend for wheeze was only significant for gases/fumes. Among subjects who did not report using coal stove heating, dust exposure was a significant predictor for FEV1, FEV1/FVC, FEF25-75, and peak expiratory flow rate (PEFR). There was also a significant decrease for FEV1 and FVC with increase of gas/fume exposure levels. Both current and former smokers appeared to be more susceptible to the effect of dusts than the never smokers.(ABSTRACT TRUNCATED AT 250 WORDS)

Postnatal changes in T-type calcium current density in rat atrial myocytes

1. Postnatal changes in Ca2+ current were studied in voltage clamped atrial myocytes isolated from Sprague-Dawley rats. T- and L-type Ca2+ currents were identified using standard electrophysiological and pharmacological techniques. Cells were studied from seven groups of male and six groups of female rats ranging in age from 3 to 14 weeks. 2. The density of atrial T-type Ca2+ current showed significant variation during postnatal development, with a maximum density reached at 4.5-5 weeks. At this age, T-current density was 1.44 +/- 0.11 pA/pF (n = 23) for cells isolated from male and 1.25 +/- 0.09 pA/pF (n = 25) for cells isolated from female animals in bathing solutions containing 2 mM-Ca2+. T-current density in atrial cells isolated from younger animals (3.5 weeks postnatal) averaged 1.22 +/- 0.06 (n = 18) and 1.00 +/- 0.05 pA/pF (n = 22) or 85 and 80% of the maximum seen at 4.5-5 weeks for male and female rats, respectively. For rats older than 13 weeks, the average T-current density in atrial cells was 0.50 +/- 0.03 (n = 18) and 0.51 +/- 0.02 pA/pF (n = 35) or 35 and 41% of the maximum seen at 4.5-5 weeks for male and female rats, respectively. 3. In contrast to the T-type current, the density of atrial L-type Ca2+ current remained unchanged in rats from 3 to 14 weeks old. L-type current averaged 8.2 +/- 0.2 (n = 134) in male and 7.9 +/- 0.2 pA/pF (n = 102) in female rats. 4. Fluctuation analysis was used to estimate single T-channel current levels in 4.5- and 7.5-week-old male rats. While the T-current density differed by 70% at these two postnatal ages, no significant difference (P > 0.2) in single channel current was found. Single channel current was 0.12 +/- 0.01 pA (n = 9) for cells from 4.5-week-old and 0.13 +/- 0.01 pA (n = 7) for cells from 7.5-week-old rats. Currents were stimulated by test pulses from -80 to -30 mV at 5 mM-Ca2+. 5. No postnatal changes were seen in either the kinetics of activation or inactivation of macroscopic T-current.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural features of the 66-kDa subunit of the energy-transducing NADH-ubiquinone oxidoreductase (NDH-1) of Paracoccus denitrificans

The structural gene of the Paracoccus denitrificans NADH-ubiquinone oxidoreductase encoding a homologue of the 75-kDa subunit of bovine complex I (NQO3) has been located and sequenced. It is located approximately 1 kbp downstream of the gene coding for the NADH-binding subunit (NQO1) [Xu, X., Matsuno-Yagi, A., and Yagi, T. (1991) Biochemistry 30, 6422-6428] and is composed of 2019 base pairs and codes for 673 amino acid residues with a calculated molecular weight of 73,159. The M(r) 66,000 polypeptide of the isolated Paracoccus NADH dehydrogenase complex is assigned the NQO3 designation on the basis of N-terminal protein sequence analysis, amino acid analysis, and immuno-cross-reactivity. The encoded protein contains a putative tetranuclear iron-sulfur cluster (probably cluster N4) and possibly a binuclear iron-sulfur cluster. An unidentified reading frame (URF3) which is composed of 396 base pairs and possibly codes for 132 amino acid residues was found between the NQO1 and NQO3 genes. When partial DNA sequencing of the regions downstream of the NQO3 gene was performed, sequences homologous to the mitochondrial ND-1, ND-5, and ND-2 gene products of bovine complex I were found, suggesting that the gene cluster carrying the Paracoccus NADH dehydrogenase complex contains not only structural genes encoding water-soluble subunits but also structural genes encoding hydrophobic subunits.

[Mechanical principles of L-trapezoid compression plate in the fixation of trochanter fractures]

Three pairs of human cadaver femur were used for simulation electric test with load on both legs and single leg. An Evans III osteotomy was made, and stabilized with L-trapezoid compression plate (L-TCP). L-angled plate (L-AP) 95 degrees and 130 degrees respectively. The results demonstrated that the stability of fixation of L-TCP was significantly greater than L-AP. Since the cancellous screw of L-TCP can hold the proximal fragment and forms a stable triangular truss with the L end, the bony support of the medial posterior part can be reconstructed by holding the lesser trochanter with the lag screw. From June 1980 to August 1990, 68 patients with 71 trochanter fractures and osteotomies were treated with L-CTP. 54 patients with 57 fractures and osteotomies were followed up for 6-52 months. All fractures and osteotomies were healed. No bone cutting off failure was encountered. The hips and knees of 51 patients (54 limbs) (94.8%) showed excellent and good functions. Infection occurred in 3 patients (4.4%). Varus deformity developed in 2 patients with an Evans IV fracture, and plate fracture occurred in one of them.