Interference of PR-bound RNA polymerase with open complex formation at PRM is relieved by a 10-base pair deletion between the two promoters

Bacteriophage lambda promoters PR and PRM direct RNA synthesis in divergent orientations from start sites 82 base pairs apart. We had previously determined that the presence on the same DNA fragment of a wild type PR promoter interfered with the utilization of the PRM promoter. The results reported here concern the effects of changing the distance between the start sites by insertion or deletion of 5 or 10 base pairs. Three different techniques (run-off transcription, gel mobility shift, and permanganate probing) were employed to monitor complex formation at PRM. Unexpectedly we find that deletion of 10 base pairs between the start sites abolishes the interference, whereas insertion of 10 base pairs does not. Deletion of 5 base pairs, however, essentially prevents joint complex formation at PR and PRM. These findings suggest several ways in which for the wild type separation of the two promoters the utilization of PRM could be affected by an RNA polymerase at PR. In addition to direct steric interference, these include the obstruction of access to DNA sites necessary for optimal contact with the RNA polymerase.

The urinary F1 activation peptide of human prothrombin is a potent inhibitor of calcium oxalate crystallization in undiluted human urine in vitro

1. The urinary F1 activation peptide of prothrombin is the predominant protein incorporated into calcium oxalate crystals precipitated from human urine. The aim of this study was to examine the effect of pure urinary prothrombin F1 on calcium oxalate crystallization in human urine. 2. Urinary prothrombin F1 was purified from demineralized calcium oxalate crystals precipitated from human urine, and its effects on calcium oxalate crystallization induced by addition of an oxalate load were tested in undiluted, ultrafiltered urine from healthy men, at final concentrations of 0 to 10 mg/l. 3. Urinary prothrombin F1 did not affect the amount of oxalate required to induce crystallization, but the volume of material deposited increased in proportion to increasing concentrations of urinary prothrombin F1. However, the mean particle size decreased in reverse order: this was confirmed by scanning electron microscopy, which showed it to be the result of a reduction in crystal aggregation rather than in the size of individual crystals. Analysis of 14C-oxalate data revealed a dose-dependent decrease in calcium oxalate deposition with an increase in urinary prothrombin F1 concentration, indicating that the increase in particle volume recorded by the Coulter Counter resulted from inclusion of urinary prothrombin F1 into the crystalline architecture, rather than increased deposition of calcium oxalate. 4. It was concluded that urinary prothrombin F1 may be an important macromolecular determinant of stone formation.

Dexniguldipine hydrochloride inhibits growth of human ht-29 colon-carcinoma cells and expression of protein-kinase-C-delta and protein-kinase-C-zeta

Previous studies have implicated protein kinase C (PKC) in colon carcinogenesis, but a clear understanding of the role of PKC in colon cancer is lacking. The purpose of this study was to investigate the effects of dexniguldipine hydrochloride (DNIG) on the in vitro growth of HT-29 human colon carcinoma cells and the expression of PKC isoforms. DNIG is a selective inhibitor of PKC that binds specifically to the regulatory region and is also a potent antineoplastic drug with an ability to reverse multidrug resistance. DNIG (1.6-25 mu M) decreased the number of HT-29 cells in culture in a time- and dose-dependent manner with an EC(50) of 1.4 mu M on day 3. Predominant PKC isoforms expressed in HT-29 cells were identified as Delta and zeta by immunoblotting. The expression of PKC Delta and zeta was inhibited significantly by DNIG (0.16-1.25 mu M). These results suggest that the suppression of the growth of HT-29 colon carcinoma cells by DNIG involves the inhibition of the expression of PKC Delta and zeta.

Contribution of B cell subsets to delayed development of MAIDS in xid mice

C57BL/6 (B6) mice develop a syndrome of progressive lymphoproliferation and immunodeficiency, murine AIDS (MAIDS), when infected with an etiologic replication-defective virus termed BM5def. Induction of MAIDS requires the presence of CD4+ T cells and B cells. B6 mice with altered conventional B cell function and a deficit in CD5+ B cells due to the xid mutation develop disease with a greatly prolonged latency. The association of this mutation with resistance to MAIDS was confirmed in studies of P.xid mice. To test the hypothesis that conventional B cells are required for rapid induction of disease, B6.xid mice were injected with spleen cells from nude mice or were given bone marrow from aged donors. Both sets of recipients developed advanced disease by 10 weeks post infection, suggesting that resistance to MAIDS in xid mutants may be due to effects of B cells other than the CD5+ subset.

Is nephrocalcin related to the urinary derivative (bikunin) of inter-alpha-trypsin inhibitor?

OBJECTIVE

To isolate, purify, sequence and characterize nephrocalcin (NC), a urinary protein that may be an important determinant of calcium oxalate (CaOx) kidney-stone disease.

MATERIALS AND METHODS

Proteins were isolated from human urine using cellulose and resin columns and were sequenced using Edman degradation and SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Inhibition of CaOx crystal growth by the isolated proteins was assessed by measuring the deposition of 14C-labelled CaOx.

RESULTS

A protein assumed to be NC on the basis of SDS-PAGE, inhibitory and gel filtration properties was isolated from healthy human urine. Its molecular weight and the amino acid sequences of two of its peptides suggested it was identical to fragment HI-14 of the light chain (bikunin) of inter-alpha-trypsin inhibitor (ITI).

CONCLUSIONS

NC represents a portion of the light chain of ITI, although this conclusion must remain tentative until confirmed using authentic NC.

Genetic analysis of the terminal 8-bp inverted repeats of transposon Tn7

Mutations in the terminal 8-bp (5'-T1G2T3G4G5G6C7G8-3') of the inverted repeats of the bacterial transposon, Tn7, were analysed by measuring Tn7 transposition to the attachment site, attTn7. The mutation, C2, present at either end of Tn7 reduces transposition only threefold, but in the double mutant, with C2 at both ends of Tn7, no transposition is detected. C6 mutations have no effect on transposition frequency. Replacement with 5'-A3C4G5C6G7C8-3' at the right end of Tn7 apparently abolishes transposition; yet in the double mutant, where the inverted repeats are restored by substituting this sequence at both ends of Tn7, transposition is partially rescued. This suggests that the mechanism of Tn7 transposition requires communication between the two ends. Tn7 transposition has always been seen to generate a 5-bp target duplication. This is presumed to result from a staggered cut, plus repair synthesis during transposition. We found that two of our right-end mutants, C2 and C6, sometimes yielded a 6-bp target duplication. This observation implies that cleavage of the target site might also involve interaction with the donor ends which, when mutant, relax the specificity for target-site cleavage.

Excitation, oscillations and wave propagation in a G-protein-based model of signal transduction in Dictyostelium discoideum

In an earlier paper (Tang & Othmer 1994 Math. Biosci 120, 25-76), we developed a G-protein-based model for signal transduction in the cellular slime mould Dictyostelium discoideum and showed that it can account for the results from perfusion experiments done by Devreotes and coworkers (Devreotes et al. 1979 J. Cell. 80, 300-309; Devreotes & Steck 1979 J. Cell Biol. 80, 300-309; Dinauer et al. 1980 J. Cell Biol. 86, 537-561). The primary experimental observables are the amounts of cAMP secreted and the time scale of adaptation in response to various stimuli, and we showed that the predictions of the model agree well with the observations. Adaptation in the model arises from dual receptor-mediated pathways, one of which produces a stimulatory G protein Gs and the other of which produces an inhibitory G protein Gi. In this paper we use the model to simulate the suspension experiments of Gerisch & Wick (1975 Biochem. biophys. Res. Commun. 65, 364-370) and the experiments done in cell cultures on Petri dishes (Tomchik & Devreotes 1981 Science, Wash. 212, 443-446). The model predicts excitation to cAMP stimuli, sustained oscillations, or spiral waves and target patterns, depending on the developmental stage of the cells and experimental conditions. The interaction between different pacemakers is also studied.

Frequency encoding in excitable systems with applications to calcium oscillations

A number of excitable cell types respond to a constant hormonal stimulus with a periodic oscillation in intracellular calcium. The frequency of oscillation is often proportional to the hormonal stimulus, and one says that the stimulus is frequency encoded. Here we develop a theory of frequency encoding in excitable systems and apply it to intracellular calcium oscillations that results from increases in the intracellular level of inositol 1,4,5-triphosphate.

Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins

Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre.

An adaptive filter for steady-state evoked responses

A 2-weight adaptive filter that determines the amplitude and phase of steady-state evoked potentials is presented. Reference signals are derived from the visual stimulator that are related to corresponding harmonics of the response and the filter weights are adjusted so as to minimize the squared estimation error between the reference and the recorded signal using the recursive least squares (RLS) method. The filter, which acts as an adaptive bandpass filter, is followed by a detector based on the T2circ statistic. The performance of the RLS adaptive filter was compared to that of the conventional Discrete Fourier Transform (DFT) and the filtered DFT of Tang and Norcia in a series of simulations with known sinusoids buried in Gaussian noise and in EEG noise. In the simulations, the RLS adaptive filter detected signals at about 3-4 times lower signal to noise ratios than did the DFT. The RLS filter also outperformed the filtered DFT. Qualitatively similar results were obtained with human visual evoked potential recordings. The adaptive RLS filter significantly outperforms both the DFT and filtered DFT and is much simpler to implement than the filtered DFT method of Tang and Norcia.

Application of adaptive filtering to steady-state evoked response

A new method to detect steady-state evoked potentials (EPs) is presented. The technique is based on a two-weight recursive least squares (RLS) adaptive filter and the Tcirc2 statistic. Simulations with known sinusoids buried in Gaussian noise and in EEG noise indicate that the adaptive filter can detect signals at 3 or 4 times lower signal-to-noise ratios that the discrete Fourier transform (DFT). Qualitatively similar results were obtained with human visual evoked potential recordings.

A new protein folding recognition potential function

On the study of protein inverse folding problem, one goal is to find simple and efficient potential to evaluate the compatibility between structure and a given sequence. We present here a novo empirical mean force potential to address the importance of electrostatic interactions in protein inverse folding study. It is based on protein main chain polar fraction and constructed in a way similar with Sippl's from a database of 64 known independent three-dimensional protein structures. This potential was applied to recognize the protein native conformations among a conformation pool. Calculated results show that this potential is powerful in picking out native conformations, in addition it can also find structure similarity between proteins with low sequence similarity. The success of this new potential clearly shows the importance of electrostatic factors in protein inverse folding studies.

QSAR of 3-methylfentanyl derivatives studied with neural networks method

AIM

To use neural networks, which simulate the functions of living nervous systems, in QSAR studies;

METHODS

Using the back-propagation neural networks program devised by us, combining with partial least squares (PLS) method, we studied the relationships of quantum chemical indices and analgesic activities of 25 3-methylfentanyl derivatives;

RESULTS

Through learning process, a good QSAR model was established, and the activities of these compounds were predicted; the correlation between the activities and quantum chemical indices: the net charge of the atom N1, the net charge of the atom O16, the torsional angle of atoms C10-C9-N8-C4, the interatomic distance between atom C7 and the center of phenyl plane C9-14 (PhA), is quite well-matched. Based on these results, an interactive pattern between 3-methylfentanyl derivatives and opioid receptors was suggested;

CONCLUSION

Not only are the results of neural networks superior to those of PLS method but they also provide accurate predictions of the activity of the compounds and also combine the PLS method with neural networks.

A model of calcium dynamics in cardiac myocytes based on the kinetics of ryanodine-sensitive calcium channels

The ryanodine-sensitive calcium channels are pivotal to signal transduction and cell function in many cell types, including cardiac myocytes. In this paper a kinetic model is proposed for these channels. In the model there are two Ca regulatory sites on the channel protein, one positive and the other negative. Cytoplasmic Ca binds to these regulatory sites independently It is assumed that the binding of Ca to the positive site is a much faster process than binding to the negative site. At steady state, the channel opening as a function of the Ca concentration is a bell-shaped curve. The model predicts the adaptation of channels to constant Ca stimulus. When this model is applied to cardiac myocytes, it predicts excitability with respect to Ca perturbations, smoothly graded responses, and Ca oscillations in certain pathological circumstances. In a spatially distributed system, traveling Ca waves in individual myocytes exist under certain conditions. This model can also be applied to other systems where the ryanodine-sensitive channels have been identified.

Refined 1.8 A resolution crystal structure of the porcine epsilon-trypsin

Porcine epsilon-trypsin is a three-chain inactivated trypsin from the limited autolysis of porcine beta-trypsin. It is cleaved at positions Lys60-Ser61 and Lys145-Ser146. The crystal structure has been determined by using the molecular replacement method, and refined at 1.8 A resolution. The R-value of final model is 0.184. Comparison with the electron density map of porcine beta-trypsin (PTRY) in complex (BBIT), and with that of native bovine beta-trypsin (HTNA), revealed no obvious changes except at the autolysis positions, and no changes at the active center were observed. The autolysis at positions Lys60-Ser61 and Lys145-Ser146 does not affect the conformation of His-57 in the active center and therefore cannot explain for a loss in porcine epsilon-trypsin activity.

3D-QSAR study on ether and ester analogs of artemisinin with comparative molecular field analysis

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to study the correlations between the physicochemical properties and the in vitro activities of a series of ether and ester analogs of artemisinin. Four alignment models were used in the CoMFA investigation. The correlations derived from CoMFA analysis with the four alignments proved all to have good predictive values. The steric field predictive model of alignment B is accordant with the experimental results of Avery M A, et al: J Med Chem 1993; 36: 4264-75. The electrostatic field predictive results of alignments A, B, and C are consistent with our previous result of quantum chemical calculation. The highest rcross2 of alignment D, indicated that the side chain of -C6-O2-O1-C10-O3-C7-O4-C12-O5- and atom C16 are important groups of artemisinin analogs for antimalarial activity.

Clonal outgrowths of T and B cells in SCID mice reconstituted with cells from mice with MAIDS

Murine acquired immunodeficiency syndrome (MAIDS), induce in mice by a defective murine retrovirus (BM5def), is characterized by development of severe immunodeficiency and polyclonal lymphoid proliferation which progress to yield oligoclonal populations of T and B cells. Oligoclonal populations transferred to SCID mice grew as clonal CD4+ T cell or B cell lineage transplants having one or more unique clonal integrations of BM5def. In some cases, spleens of single donor mice were shown to contain both B cell and T cell lineage clones that could be transferred individually after separation and were clonally unrelated. Successful transplants were obtained from oligoclonal populations as early as 63 days after infection. Mouse strains both sensitive or moderately resistant to MAIDS yielded clonal transplants.