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Selective inhibition of in vitro DNA synthesis dependent on phiX174 compared with fd DNA. I. Protein requirements for selective inhibition.

Crude extracts of Escherichia coli selectively convert fd viral DNA and not phiX174 DNA to duplex DNA via a complex series of reactions one of which involves RNA polymerase. Reactions leading to formation of fd duplex-replicative (RFII) structures have been reconstituted with purified proteins from E. coli. Maximal synthesis requires the combined action of E. coli binding protein, DNA elongation factor I, DNA elongation factor II preparations (which are a mixture of dna Z and DNA elongation factor III), DNA polymerase III, DNA-dependent RNA polymerase, Mg2+, dATP, dGTP, dCTP, dTTP, and ATP, GTP, CTP, and UTP. In contrast to crude extracts of E. coli, purified protein fractions do not distinguish between fd DNA and phiX174 DNA in duplex DNA formation. The addition of crude fractions of E. coli to the purified components listed above selectively permits fd RFII formation and prevents phiX RFII formation. This selective inhibition was used as an assay to isolate proteins essential for this phenomenon; they include RNase H, discriminatory factor alpha, and discriminatory factor beta.

Adenosine Triphosphatases↗

Using an evidence-based approach for system selection at a large academic medical center: lessons learned in selecting an ambulatory EMR at Mount Sinai Hospital.

The experience of Mount Sinai Hospital is representative of the challenges and problems facing large academic medical centers in selecting an ambulatory EMR. The facility successfully revived a stalled process in a challenging financial climate, using a framework of science and rigorous investigation. The process incorporated several innovations: 1) There was a thorough review of medical informatics literature to develop a mission statement, determine practical objectives and guide the demonstration process; 2) The process involved rigorous investigation of vendor statements, industry statements and other institution's views of vendors; 3) The initiative focused on user-centric selection, and the survey instrument was scientifically and specifically designed to assess user feedback; 4) There was scientific analysis of validated findings and survey results at all steering meetings; 5) The process included an assessment of vendors' ability to support research by identifying funded and published research; 6) Selection involved meticulous total cost of ownership analysis to assess and compare real costs of implementing a vendor solution; and finally, 7) There were iterative meetings with stakeholders, executives and users to understand needs, address concerns and communicate the vision.

Academic Medical Centers↗

Evidence for rapid selection and deletion of HIV-1 subpopulations in vivo by V3-specific neutralizing antibody: a model of humoral-associated selection.

Emergence in two chimpanzees of HIV-1 HTLV-IIIB variants resistant to neutralization by the pre-existing antibody is described. Viruses isolated from the HTLV-IIIB gp120 vaccinated and challenged animal were more resistant to neutralization, had more heterogenic genomes and showed more pronounced antigenic drift as determined by serotypic neutralization analysis than viruses isolated from the naive infected animal, indicating immune pressure as the selective mechanism. The earliest selecting antibody population detected in the chimpanzees appeared to be conformationally dependent. This was demonstrated by its ability to neutralize only the most replication-competent sub-populations of the HTLV-IIIB inoculum strain, yet was found to bind a HTLV-IIIB common nonapeptide (IQRGPGRAF) derived from the gp120 isolate-specific 3rd variable domain (V3) also known to induce isolate-specific neutralization in multiple species. Each of the recovered isolates had become resistant to neutralization by both a monoclonal (0.5 beta) and polyclonal HTLV-IIIB gp120 V3-specific antibody by as much as 16 to 256-fold. Amplification of the V3 coding sequence by polymerase chain reaction and subsequent sequence analysis of the neutralization-resistant variants obtained from in vivo infected animals indicated that resistance to neutralization was conferred by changes outside the direct binding site for the selective neutralizing antibody. Further studies indicated that apparent neutralization-resistant variants, yielded after in vitro passage through chimpanzee and human peripheral blood mononuclear cell cultures void of HIV-specific antibody, result from the homogenic amplification of the more replication competent sub-population pre-existing in the original viral stock. These faster replicating sub-populations appear to dominate initially and therefore are the initial prime targets recognized by the chimpanzee humoral immune system upon infection in vivo and thus eliminated. The described finding of virus escape due to a conformationally-induced flexibility of the major neutralization epitope termed "conformational-V3 hypervariability", coupled to the known primary amino acid hypervariability of this epitope (V3) termed "linear-V3 hypervariability", may be all that is required by the virus to survive in an otherwise effective humoral immune system.

Amino Acid Sequence↗

Potent and selective inhibition of human nitric oxide synthases. Selective inhibition of neuronal nitric oxide synthase by S-methyl-L-thiocitrulline and S-ethyl-L-thiocitrulline.

Potent and selective inhibition of neuronal nitric oxide synthase (nNOS) compared to endothelial NOS (eNOS) and inducible NOS (iNOS) may be useful to treat cerebral ischemia (stroke) and other neurodegenerative diseases. S-Methyl-L-thiocitrulline (Me-TC) and S-ethyl-L-thiocitrulline (Et-TC) inhibited the oxidation of L-arginine and the L-arginine-independent oxidation of NADPH by nNOS from human brain. Me-TC and Et-TC were slow, tight binding inhibitors of nNOS with second-order association rate constants (kon) of 2.6 x 10(5) M-1 s-1 and 1.3 x 10(5) M-1 s-1, respectively. The respective dissociation rate constants (koff) were 3 x 10(-4) s-1 and 0.7 x 10(-4) s-1. Thus, the Kd values calculated from koff/kon were 1.2 and 0.5 nM, respectively. L-Arginine was a competitive inhibitor of Me-TC and Et-TC binding with competition constant (Ks) values of 2.2 and 2.7 microM, respectively. The Km of nNOS for L-arginine was 1.6 microM. The active site concentration of nNOS was estimated by titration with Et-TC. Based on this active site concentration, a kcat of 0.4 s-1 for the oxidation of L-arginine, was calculated. Me-TC and Et-TC were less potent inhibitors of human iNOS (Ki values of 34 and 17 nM, respectively) and human eNOS (Ki values of 11 and 24 nM). Thus, Me-TC and Et-TC were 10- and 50-fold, respectively, more potent inhibitors of nNOS than eNOS. Furthermore, Me-TC was also 17-fold selective for rat nNOS in neuronal tissue compared to rat eNOS in vascular endothelium, suggesting that Me-TC may be selective for nNOS in vivo and therefore, may be therapeutically useful to treat neurodegenerative diseases.

Amino Acid Oxidoreductases↗

Use of selective antagonists for further characterization of tachykinin NK-2, NK-1 and possible "septide-selective" receptors in guinea pig bronchus.

NK-1 and NK-2 tachykinin receptors in guinea pig airways appear to have some unusual characteristics. The analog [pGlu6,Pro9] SP(6-11) (septide) may also act on atypical NK-1 receptors in guinea pig ileum. In this study, we used new tachykinin antagonists to investigate further the receptors in the guinea pig bronchus. In the presence of 1 microM indomethacin and phosphoramidon, the selective agonists [Sar9,Met(O2)11]-SP and [Pro9]-SP (both NK-1), [Lys5,MeLeu9,Nle10]-NKA(4-10) (NK-2) and septide were full agonists, with pD2 values of 8.00, 7.78, 9.11 and 8.52, respectively on epithelium-intact preparations. Contractions to septide were unaffected by atropine (5 microM) and tetrodotoxin (1 microM). Denudation of epithelium significantly enhanced the potency of [Sar9,Met(O2)11]-SP and [Pro9]-SP but not of septide and [Lys5,MeLeu9,Nle10]-NKA(4-10). The potency order for NK-2-selective antagonists against [Lys5,MeLeu9,Nle10]-NKA(4-10) was GR 94800 > SR 48968 MDL 29913 > MEN 10207 (pA2 values 8.97, 8.73, 7.11 and 6.49, respectively). The NK-1 selective antagonists, OP 96345, GR 82334 and RP 67580 were weak or ineffective against [Sar9,Met(O2)11]-SP and [Pro9]-SP (pA2 6.69 or less), whereas they were more than one order of magnitude more potent against septide (pA2, 7.78, 7.48 and 6.58, respectively). In epithelium-denuded bronchi, the antagonist potency of GR 82334 was unchanged. These data indicate that septide interacts with tachykinin receptors in guinea pig bronchial smooth muscle in a manner different from that of [Sar9,Met(O2)11]-SP and [Pro9]-SP, and provide some evidence for heterogeneity of NK-1 receptors in the guinea pig airways.

Amino Acid Sequence↗

Solution conformation of mu-selective dermorphin and delta-selective deltorphin-I in phospholipid micelles, studied by NMR spectroscopy and molecular dynamics simulations.

Complete proton resonance assignments of the naturally occurring mu-selective dermorphin (H-Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2) and delta-selective deltorphin-I (H-Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2) were carried out by two-dimensional 1H-NMR techniques to investigate the conformational features in the membrane-mimetic micelles of perdeuterated dodecylphosphocholine. Fifty possible three-dimensional structures for respective peptides were generated by means of distance geometry calculations, all of which satisfy the proton-proton distances derived from NOE measurements within the allowable range, and 25 of them were subjected to the molecular dynamics simulations for 10 ps, in which the NOE distances were included as the energetic constraints. Although conformers simulated for dermorphin showed relatively large conformational variations because of the limited NOE data, most of them were characterized as an entirely folded structure bent at the Gly4 residue, where each of the N- and C-terminal tetrapeptides took an extended conformation. On the other hand, most conformations of deltorphin-I showed the common feature that the N-terminal Tyr-D-Ala-Phe-Asp and C-terminal Val-Val-Gly-NH2 sequences took respective folded conformations, and these were almost at right angles on the border of the Asp-Val sequence. These conformational characteristics are discussed in terms of the possible relationship with the mu/delta-opioid receptor selectivity.

Amino Acid Sequence↗

Weekly KT/V urea and selected outcome criteria in 56 randomly selected CAPD patients.

The optimal way to objectively measure the adequacy of continuous ambulatory peritoneal dialysis (CAPD) therapy remains controversial. It has been suggested that one-third or more of all CAPD patients are presently receiving "inadequate dialysis" when dialysis prescriptions are not carefully calculated. To better define the therapy being delivered in a large, freestanding CAPD center, weekly KT/V urea and creatinine clearance per 1.73 m2 body surface area were measured in 56 of 180 patients randomly selected from our unit in whom dialysis prescriptions were arbitrarily determined by nurses and physicians. In addition, protein catabolic rates and selected clinical outcome criteria were assessed. Weekly KT/V urea correlated with weekly creatinine clearance (r = 0.50) as well as with the protein catabolic rate (r = 0.45). Patients were arbitrarily divided into three groups based on KT/V urea measurements. Thirty percent of the patients had weekly KT/Vs < or = 1.4, 41% had KT/Vs between 1.5 and 1.8, and 29% had weekly KT/Vs > or = 1.9. Significant differences were not noted in hospitalization rates, erythropoietin doses, or serum albumin concentrations in patients with KT/Vs < or = 1.4 and in patients with KT/Vs > or = 1.9. Peritonitis rates were highest in the patients with KT/V > or = 1.9. Therefore, in patients randomly selected from our large CAPD center, 30% of the patients had weekly KT/V urea measurements < or = 1.4. The clinical significance of this finding remains uncertain.

Adult↗

Actions of A-131701, a novel, selective antagonist for alpha-1A compared with alpha-1B adrenoceptors on intraurethral and blood pressure responses in conscious dogs and a pharmacodynamic assessment of in vivo prostatic selectivity.

A-131701 (3-[2-((3aR,9bR)-cis-6-methoxy-2,3,3a,4,5,9b, hexahydro-[1H]-benz[e]isoindol-2-yl)ethyl]pyrido [3',4': 4,5]thieno[3,2-d]pyrimidine-2,4(1H,3H)-dione) is a novel compound previously shown to be selective for alpha-1a sites compared with alpha-1b adrenoceptors in radioligand binding studies and isolated tissue bioassays and to block canine urethral pressure (IUP) responses to exogenous alpha-1 adrenergic agonists to a greater extent than blood pressure responses. In conscious dogs in which IUP and mean arterial blood pressure (MABP) responses were measured periodically up to 24 hr, A-131701 blocked phenylephrine (PHE)-induced increases in IUP to a greater extent than MABP responses, and the blockade of the IUP effects of PHE was significantly different from control for up to 12 hr after doses greater than 0.3 mg/kg p.o., whereas blood pressure effects were of a lesser extent and duration. In addition to the weak antagonism of PHE-induced blood pressure responses, A-131701 also exhibited minimal effects on basal blood pressure in the dog, unlike terazosin, doxazosin or tamsulosin. Pharmacokinetic analysis of plasma samples from dogs indicated that A-131701 had a half-life of 0.4 to 0.8 hr and a bioavailability of 30 to 50% in dogs. Somewhat longer half-lives were observed in rat and monkey, with bioavailability values in the 25 to 30% range. Evidence of nonlinearity of pharmacokinetics was obtained in dogs and monkeys. Pharmacodynamic analysis revealed differences between A-131701 and nonselective alpha-1 adrenoceptor antagonists in selectivity for prostatic versus vascular alpha-1 adrenoceptors based on either extent or duration of blockade, which were either similar to or superior to compounds such as tamsulosin or REC 15/2739. These data demonstrate that A-131701 selectively blocks canine prostatic alpha-1 adrenoceptors for prolonged periods compared with MABP responses in vivo. Therefore, A-131701 should have clinical utility in the pharmacotherapy of benign prostatic hyperplasia.

Adrenergic alpha-1 Receptor Antagonists↗

Selection in complex genetic systems. VI. Equilibrium properties of two locus selection models with partial selfing.

The results of a combined analytical and numerical study of two locus selection models with partial selfing indicate that several commonly held opinions about the effects of partial self-fertilization do not hold in general. For example, the heterozygosity of a population may actually increase as the selfing rate is increased. Similarly, selection strong enough to guarantee a two locus polymorphism with complete selfing does not necessarily guarantee a two locus polymorphism with intermediate amounts of self-fertilization. The results presented here and a brief review of previously existing results indicate that the predictions of population genetic models based on the assumption of random mating will not be greatly altered by a small amount of self-fertilization, unless the loci involved are tightly linked. On the other hand, the results presented indicate that a very small amount of outcrossing may lead to marked differences from the expectation based on complete self-fertilization.

Biometry↗

Pelvic lymphadenectomy can be omitted in selected patients with carcinoma of the prostate: development of a system of patient selection.

OBJECTIVES: The prevalence of pelvic lymph node metastases in men with clinically localized prostate cancer has decreased dramatically over the past decade, possibly due to efforts at early detection. With a significantly lower incidence of pelvic node involvement, it may be possible to identify a segment of patients for whom pelvic lymph node dissection (PLND) may be omitted. This study was conducted to develop a method to select patients for whom PLND could be omitted. METHODS: We analyzed serum prostate-specific antigen (PSA), clinical stage, biopsy Gleason score, and final pathologic stage in 481 men with clinically localized prostate cancer. These variables were compared to the risk of positive pelvic lymph nodes. RESULTS: Logistic regression analysis determined that combining all three variables provided the best determination of final pathologic stage. A series of probability curves have been created to estimate the risk of positive lymph nodes in a given patient. Based on the distribution of patients in this study and using these probability functions, PLND could be avoided in up to 50% of patients with localized prostate cancer diagnosed by contemporary methods. CONCLUSIONS: In properly selected patients, pelvic lymphadenectomy can be omitted in the staging and treatment of localized prostate cancer.

Humans↗

A simultaneous evaluation method of purity and apparent stability constant of Ca-chelating agents and selectivity coefficient of Ca-selective electrodes.

To determine the purity (q) of Ca-chelating agents (such as EGTA and BAPTA) and their apparent stability constants to Ca2+ (K') using Ca(2+)-selective electrodes precisely, we have developed a new method using the double-log optimization. Free Ca2+ concentration was plotted against the ratio of the concentrations of Ca(2+)-bound to Ca(2+)-free chelator on double logarithmic co-ordinates in which a linear relationship with a slope of -1 must hold for the metal-chelator reaction with a stoichiometry of 1 to 1. Not only the q and K' values but also the selectivity coefficient of the electrode could be simultaneously estimated on the double-log plot through an optimizing method. Error analyses using a Monte Carlo simulation showed that the double-log plot is statistically more reliable and robust than the Scatchard plot and that the optimizing method is more objective and reliable than previous methods involving extrapolation and truncation procedures.

Calcium↗

New ccdB positive-selection cloning vectors with kanamycin or chloramphenicol selectable markers.

Recently, we described pKIL18/19 positive-selection cloning vectors which rely on the inactivation of the cytotoxic ccdB gene [Bernard et al., Gene 148 (1994) 71-74]. They are new tools for simplifying gene cloning/sequencing procedures, as only recombinant DNA allow the formation of viable colonies. To enhance positive-selection capabilities, putative translational reinitiation codons located within the pKIL18/19 ccdB were modified by site-directed mutagenesis. New pKIL-derived vectors with kanamycin (KmR) or chloramphenicol (CmR) resistance-encoding genes were also constructed. In addition, a new host derived from the DH2 strain was developed.

Bacterial Proteins↗

The use of selective estrogen receptor modulators and selective estrogen receptor down-regulators in breast cancer.

Tamoxifen is one of the most effective treatments for breast cancer through its ability to antagonize estrogen-dependent growth by binding estrogen receptors (ERs) and inhibiting proliferation of breast epithelial cells. However, tamoxifen has estrogenic agonist effects in other tissues such as bone and endometrium due to liganded ER activating target genes in these different types of cell. Several novel anti-estrogen compounds have been developed which have a reduced agonist profile on breast and gynaecological tissues. These compounds offer the potential for enhanced efficacy and reduced toxicity compared with tamoxifen. In advanced breast cancer clinical data exist for two groups of agents: the selective estrogen receptor modulators (SERMs), further divided into "tamoxifen-like" (e.g. toremifene, droloxifene and idoxifene) and "fixed ring" compounds (e.g. raloxifene, arzoxifene and EM-800), and the selective estrogen receptor down-regulators (SERDs; e.g. fulvestrant (ICI 182780), SR 16234 and ZK 191703) also termed "pure anti-estrogens". In phase II trials in tamoxifen-resistant metastatic breast cancer the SERMs show low objective response rates (range 0-15%), suggesting cross resistance with tamoxifen. Randomized phase III trials for toremifene and idoxifene in over 1500 patients showed no significant difference compared with tamoxifen. Fewer clinical data exist for the "fixed ring" SERMs and it remains unclear whether any clinical advantage exists for the "fixed ring" SERMs over tamoxifen as first-line therapy. The main advantage for SERMs such as tamoxifen and raloxifene probably remains in early-stage disease (adjuvant therapy or prevention). Fulvestrant and the other SERDs have a high affinity for the estrogen receptor (ER) compared to tamoxifen, but none of its agonist activities. Of the SERDs, only fulvestrant has entered the clinic and this new agent is showing promising clinical activity in the treatment of advanced breast cancer. Recently published phase III studies have shown fulvestrant to be at least as effective as the third-generation aromatase inhibitor anastrozole in patients whose disease has relapsed or progressed on prior endocrine therapy. Surprisingly, however, in a phase III trial versus tamoxifen for the first-line therapy of advanced breast cancer fulvestrant did not attain the requirements for equivalence to tamoxifen, and in terms of time-to-treatment failure was inferior (5.9 versus 7.8 months for fulvestrant and tamoxifen, respectively; P=0.029). Future clinical studies will evaluate fulvestrant in the neoadjuvant setting together with its optimal sequencing in relation to tamoxifen and other endocrine therapies in advanced disease.

Antineoplastic Agents, Hormonal↗

Selective estrogen receptor modulators with conformationally restricted side chains. Synthesis and structure-activity relationship of ERalpha-selective tetrahydroisoquinoline ligands.

We disclose herein the discovery of estrogen receptor alpha (ERalpha) selective estrogen receptor modulators (SERMs) of the tetrahydroisoquinoline series that incorporate novel conformationally restricted side chains as replacement of the aminoethoxy residue typical of SERMs. Molecular modeling studies used in conjunction with the X-ray crystal structure of the ERalpha ligand binding domain (LBD) with raloxifene (7) suggested a diazadecaline moiety as a viable mimic of the SERM side chain. On the basis of this knowledge, the piperidinylethoxy moiety of our lead compound 60 was replaced by a diazadecaline subunit, providing the novel tetrahydroisoquinoline 29. In addition to exhibiting a binding affinity to ERalpha and antagonistic properties in the estrogen response element and MCF-7 assays similar to those of the parent compound 60, ligand 29 showed a reduced agonist behavior in the MCF-7 assay in the absence of 17beta-estradiol. These data point toward the fact that 29 may have a potential for breast cancer prevention/treatment in vivo, a feature which is particularly attractive in the quest for safe alternatives to hormone replacement therapy. In a pharmacokinetic experiment carried out in rats, 29 displayed an interesting profile, with a bioavailability of 49%. We also disclose the X-ray crystal structure of 29 in complex with ERalpha-LBD, which reveals the preferred configurations of 29 at the two chiral centers and the details of its interactions with the receptor. Finally, our structure-activity relationship studies show that other analogues bearing constrained side chains retain potency and antagonist activity and that a 3-OH substituted phenyl D-ring increases the selectivity of a set of piperazinyl-containing ligands in favor of ERalpha over ERbeta.

Animals↗

Selection during a selfing programme. II. The effects of two or more rounds of selection.

Theory presented in a previous paper has been used to provide a description of the responses expected from selection in two or more generations of a selfing series. Optimum two-stages and multi-stage selection programmes are described, for a limited set of circumstances, and compared with the single-stage designs described previously. Simulations show that biases may be expected if epistasis is present or if the number of effective factors is small. If the number of effective factors is large, then progress from even the most efficient designs will be limited by drift.

Breeding↗

Signatures of selection? Patterns of microsatellite diversity on a chromosome containing a selected locus.

This paper explores patterns of genetic diversity near a locus known to have been under selection. The myostatin gene (GDF-8) has been shown to be associated with double muscling, a phenotype selected for in a number of cattle breeds. We examined population genetic parameters for microsatellite loci at varying distances from GDF-8 in double-muscled (DM) and non-double-muscled (non-DM) cattle breeds in order to assess patterns of diversity. A theoretical analysis was also performed to predict the patterns of diversity expected under different scenarios. We found differences in the patterns of heterozygosity, allele diversity and linkage disequilibrium between DM and non-DM breeds. However, there were some exceptions to the predicted patterns. These are discussed in light of the histories of the breeds and the potential for using microsatellite diversity for mapping trait genes in livestock populations.

Animals↗

Selection-subtraction approach (SSA): a universal genetic screening technique that enables negative selection.

Screening of expression libraries for bioactive clones that modulate the growth of mammalian cells has been limited largely to positive selections incapable of revealing growth suppressive or lethal genetic elements. We have developed a technique, selection-subtraction approach (SSA), that allows growth-modulating clones to be isolated based on alterations in their relative abundance in growing cell populations that have been transduced with an expression library. SSA utilizes tagged retroviral libraries in bacteriophage lambda vectors (retrophages). Nylon prints from retrophage libraries are used to determine the relative abundance of tags in library-transduced cells to identify biological activity of individual clones. Applications of SSA for gene discovery, target discovery, and generation of mutant proteins have been demonstrated, by using p53 and ataxia telangiectasia mutated (ATM) as models to isolate growth inhibitory proteins, peptides and antisense RNAs, and temperature-sensitive mutant proteins.

Base Sequence↗

Selection in finite populations with multiple alleles. 3. Genetic divergence with centripetal selection and mutation.

Natural selection for an intermediate level of gene or enzyme activity has been shown to lead to a high frequency of heterotic polymorphisms in populations subject to mutation and random genetic drift. The model assumes a symmetrical spectrum of mutational variation, with the majority of variants having only minor effects on the probability of survival. Each mutational event produces a variant which is novel to the population. Allelic effects are assumed to be additive on the scale of enzyme activity, heterosis arising whenever a heterozygote has a mean level of activity closer to optimal than that of other genotypes in the population.-A new measure of genetic divergence between populations is proposed, which is readily interpreted genetically, and increases approximately linearly with time under centripetal selection, drift and mutation. The parameter is closely related to the rate of accumulation of mutational changes in a cistron over an evolutionary time span.-A survey of published data concerning polymorphic loci in man and Drosophila suggests than an alternative model, based on the superiority of hybrid molecules, is not of general importance. Thirteen loci giving rise to hybrid zones on electrophoresis have a mean heterozygote frequency of 0.22 +/-.06, compared with a value of 0.23 +/-.04 for 16 loci classified as producing no hybrid enzyme.

Alleles↗