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PubMed2000

Microcirculatory network structures and models.

Terminal vascular beds exhibit a high degree of heterogeneity. Pertinent parameters are nonlinearly related, and their distributions are not independent. The classical "typical vessel" approach using averaged values for different vessel classes may not lead to a correct understanding of physiology and pathophysiology of terminal vascular beds. Such problems can be avoided by studying microcirculatory functions at the network level using a combination of experiments and theoretical models. In this approach, distributions and relationships of pertinent parameters are measured in vivo, leading to the development of comprehensive databases. Such databases can be analyzed and complemented by suitable mathematical models, permitting estimation of parameters that are difficult to measure, and critical assessment of quantitative theories and hypotheses for microvascular function. This collaborative process between experimentally and theoretically oriented investigators may be facilitated in the future by the development of web-based repositories of experimental data and theoretical models.

Adaptation, Physiological↗

PubMed2005

Recombinant CYP3A417 is defective in metabolizing the hypertensive drug nifedipine, and the CYP3A417 allele may occur on the same chromosome as CYP3A5*3, representing a new putative defective CYP3A haplotype.

Genetic variation in CYP3A activity may influence the rate of the metabolism and elimination of CYP3A substrates in humans. We previously reported four new CYP3A4 coding variants in three different racial groups. In the present study, we examined metabolism of nifedipine by the recombinant forms of these allelic variants. Metabolism of nifedipine by the L293P (CYP3A4*18), M445T (CYP3A4*3), and P467S (CYP3A4*19) allelic variants was not significantly different from wild-type CYP3A4*1. However, F189S (CYP3A4*17) exhibited a >99% decrease in both V(max) and CL(max) of nifedipine compared with CYP3A4*1. Of 72 racially diverse individuals, CYP3A4*17 was identified in 1 of 24 Caucasian samples [1:5 Eastern European (Adygei ethnic group)]. Genotyping of an extended set of 276 genomic DNAs of Caucasians (100 from the Coriell Repository and an additional 176 from the United States) for CYP3A4*17 detected no additional individuals containing the CYP3A4*17 allele. However, additional genotyping of four more Adygei samples available from Coriell detected an additional individual carrying the CYP3A4*17 allele. New specific polymerase chain reaction-restriction fragment length polymorphism genotyping procedures were developed for the major splice variant of CYP3A5 (CYP3A5*3) and CYP3A4*17. Genotyping revealed that the two individuals carrying CYP3A4*17 were either homozygous or heterozygous for the more frequent CYP3A5*3 allele, suggesting that the two alleles may exist on the same chromosome as a new putative CYP3A poor metabolizer haplotype. We predict that individuals who are homozygous for defective alleles of both of these genes would metabolize CYP3A substrates poorly. The new genetic tests will be useful in future clinical studies to investigate genotype/phenotype associations.

Algorithms↗

PubMed2006

Preferential inhibition of the magnesium-dependent strand transfer reaction of HIV-1 integrase by alpha-hydroxytropolones.

Integration is a crucial step in the life cycle of human immunodeficiency virus type 1 (HIV-1); therefore, inhibitors of HIV-1 integrase are candidates for antiretroviral therapy. Two 7-hydroxytropolone derivatives (alpha-hydroxytropolones) were found to inhibit HIV-1 integrase. A structure-activity relationship investigation with several tropolone derivatives from The National Cancer Institute compound repository demonstrated that the 7-hydroxy group is essential for integrase inhibition. alpha-Hydroxytropolones preferentially inhibit strand transfer and are inhibitory both in the presence of magnesium or manganese. Lack of inhibition of disintegration in the presence of magnesium coupled with results from different cross-linking assays suggests alpha-hydroxytropolones as interfacial inhibitors. We propose that alpha-hydroxytropolones chelate the divalent metal (Mg2+ or Mn2+) in the enzyme active site. The most active compound against HIV-1 integrase in biochemical assays [2,4,6-cycloheptatrien-1-one, 2,7-dihydroxy-4-isopropyl (NSC 18806) IC50 = 4.8 +/- 2.5 microM] exhibits weak cytoprotective activity against HIV-1(IIIB) in a cell-based assay. alpha-Hydroxytropolones represent a new family of inhibitors for the development of novel drugs against HIV infection.

Catalytic Domain↗

PubMed2006

A three-dimensional quantitative structure-activity relationship study of the inhibition of the ATPase activity and the strand passing catalytic activity of topoisomerase IIalpha by substituted purine analogs.

Based on the topoisomerase IIalpha catalytic inhibitory activity of a previous hit compound, NSC35866, we screened 40 substituted purines or purine-like compounds from the National Cancer Institute repository for their ability to inhibit the ATPase activity of human topoisomerase IIalpha. Several compounds, including NSC348400, NSC348401 and NSC348402, were inhibitory at submicromolar concentrations. Three-dimensional quantitative structure-activity relationship models using comparative molecular field and comparative molecular similarity indices analyses were constructed using 24 of these compounds. The ability of 10 selected compounds to inhibit the complete DNA strand passage reaction of topoisomerase IIalpha correlated well with their potency as ATPase inhibitors. None of the 40 compounds significantly increased levels of the topoisomerase IIalpha-DNA covalent complex, suggesting that they functioned as catalytic topoisomerase II inhibitors and not as topoisomerase II poisons. Although some of these compounds could antagonize the effect of etoposide on the level of topoisomerase IIalpha-DNA covalent complex formation in vitro, in contrast to NSC35866, they were not capable of antagonizing etoposide-induced cytotoxicity and DNA strand breaks in cells. Two independently selected human SCLC cell lines with reduced topoisomerase IIalpha expression displayed cross-resistance to NSC348400, NBSC348401, and NSC348402, whereas an MDR1 line was fully sensitive. These results suggest that topoisomerase IIalpha is a functional cellular target for most of these substituted purine compounds and that these compounds do not display MDR1 liability.

Adenosine Triphosphatases↗

PubMed1997

P-glycoprotein substrates and antagonists cluster into two distinct groups.

To gather further insight into the interaction between P-glycoprotein (Pgp) and its substrates, 167 compounds were analyzed in multidrug resistant human colon carcinoma cells. These compounds were selected from the National Cancer Institute Drug Screen repository using computer-generated correlations with known Pgp substrates and antagonists. The compounds were prospectively defined as Pgp substrates if cytotoxicity was increased > or =4-fold by the addition of cyclosporin A (CsA) and as Pgp antagonists if inhibition of efflux increased rhodamine accumulation by 4-fold. Among the 84 agents that met either criterion, 35 met only the criterion for substrates, 42 met only the criterion for antagonists, and only seven met both criteria. Thus, compounds interacting with Pgp form two distinct groups: one comprising cytotoxic compounds that are transported and have poor or no antagonistic activity and a second comprising compounds with antagonistic activity and no evidence of significant transport. Vinblastine accumulation and kinetic studies performed on a subset of 18 compounds similarly differentiated substrates and antagonists, but inhibition of 3H-azidopine labeling and induction of ATPase activity did not. These data support an emerging concept of Pgp in which multiple regions instead of specific sites are involved in drug transport.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2002

Identification of a potent and selective pharmacophore for Cdc25 dual specificity phosphatase inhibitors.

Small molecules provide powerful tools to interrogate biological pathways but many important pathway participants remain refractory to inhibitors. For example, Cdc25 dual-specificity phosphatases regulate mammalian cell cycle progression and are implicated in oncogenesis, but potent and selective inhibitors are lacking for this enzyme class. Thus, we evaluated 10,070 compounds in a publicly available chemical repository of the National Cancer Institute for in vitro inhibitory activity against oncogenic, full-length, recombinant human Cdc25B. Twenty-one compounds had mean inhibitory concentrations of <1 microM; >75% were quinones and >40% were of the para-naphthoquinone structural type. Most notable was NSC 95397 (2,3-bis-[2-hydroxyethylsulfanyl]-[1,4]naphthoquinone), which displayed mixed inhibition kinetics with in vitro K(i) values for Cdc25A, -B, and -C of 32, 96, and 40 nM, respectively. NSC 95397 was more potent than any inhibitor of dual specificity phosphatases described previously and 125- to 180-fold more selective for Cdc25A than VH1-related dual-specificity phosphatase or protein tyrosine phosphatase 1b, respectively. Modification of the bis-thioethanol moiety markedly decreased enzyme inhibitory activity, indicating its importance for bioactivity. NSC 95397 showed significant growth inhibition against human and murine carcinoma cells and blocked G(2)/M phase transition. A potential Cdc25 site of interaction was postulated based on molecular modeling with these quinones. We propose that inhibitors based on this chemical structure could serve as useful tools to probe the biological function of Cdc25.

Amino Acid Motifs↗

PubMed2003

Stability of peroxide-containing uranyl minerals.

Minerals containing peroxide are limited to studtite, (UO2)O2(H2O)4, and metastudtite, (UO2)O2(H2O)2. High-temperature oxide-melt solution calorimetry and solubility measurements for studtite (standard enthalpy of formation at 298 kelvin is -2344.7 +/- 4.0 kilojoules per mole from the elements) establishes that these phases are stable in peroxide-bearing environments, even at low H2O2 concentrations. Natural radioactivity in a uranium deposit, or the radioactivity of nuclear waste, can create sufficient H2O2 by alpha radiolysis of water for studtite formation. Studtite and metastudtite may be important alteration phases of nuclear waste in a geological repository and of spent fuel under any long-term storage, possibly at the expense of the commonly expected uranyl oxide hydrates and uranyl silicates.

Journal Article↗

PubMed2006

Early Cretaceous spider web with its prey.

The orb web is a spectacular evolutionary innovation that enables spiders to catch flying prey. This elegant, geometric structure is woven with silk fibers that are renowned for their superior mechanical properties. We used silk gland expression libraries to address a long-standing controversy concerning the evolution of the orb-web architecture. Contrary to the view that the orb-web design evolved multiple times, we found that the distribution and phylogeny of silk proteins support a single, ancient origin of the orb web at least 136 million years ago. Furthermore, we substantially expanded the repository of silk sequences that can be used for the synthesis of high-performance biomaterials.

Amber↗

PubMed2006

Silk genes support the single origin of orb webs.

Animals↗

PubMed1965

COMPUTERIZED BIBLIOGRAPHIC SERVICES FOR BIOMEDICINE.

By its development of improved media for dissemination of information, the National Library of Medicine is fostering a greater awareness and a better understanding of research and development efforts in behalf of public health and clinical medicine, and a more rapid translation of research into clinical application. The library's transformation from a passive repository of information to an active ally of the researcher, teacher, and clinician has led to increased use of medical library facilities and has stimulated thinking through better communication of published information. The library's success in using automation for bibliographic control of medical literature suggests that other disciplines that have not already developed automated techniques of literature-reference retrieval might profitably do so.

Abstracting and Indexing↗

PubMed1991

Electronic data publishing and GenBank.

GenBank, the national repository for nucleotide sequence data, has implemented a new model of scientific data management, which we term electronic data publishing. In traditional publishing, both scientific conclusions and supporting data are communicated via the printed page, and in electronic journal publishing, both types of information are communicated via electronic media. In electronic data publishing, by contrast, conclusions are published in a journal while data are published via a network-accessible, electronic database.

Base Sequence↗

PubMed1990

The concept of probability in safety assessments of technological systems.

Safety assessments of technological systems, such as nuclear power plants, chemical process facilities, and hazardous waste repositories, require the investigation of the occurrence and consequences of rare events. The subjectivistic (Bayesian) theory of probability is the appropriate framework within which expert opinions, which are essential to the quantification process, can be combined with experimental results and statistical observations to produce quantitative measures of the risks from these systems. A distinction is made between uncertainties in physical models and state-of-knowledge uncertainties about the parameters and assumptions of these models. The proper role of past and future relative frequencies and several issues associated with elicitation and use of expert opinions are discussed.

Equipment Design↗

PubMed1997

Seed banks and molecular maps: unlocking genetic potential from the wild.

Nearly a century has been spent collecting and preserving genetic diversity in plants. Germplasm banks-living seed collections that serve as repositories of genetic variation-have been established as a source of genes for improving agricultural crops. Genetic linkage maps have made it possible to study the chromosomal locations of genes for improving yield and other complex traits important to agriculture. The tools of genome research may finally unleash the genetic potential of our wild and cultivated germplasm resources for the benefit of society.

Chromosome Mapping↗

PubMed1998

Anomalous strain accumulation in the yucca mountain area, nevada

Global Positioning System (GPS) surveys from 1991 to 1997 near Yucca Mountain, Nevada, indicate west-northwest crustal elongation at a rate of 1.7 +/- 0.3 millimeters per year (1final sigma) over 34 kilometers, or 50 +/- 9 nanostrain per year. Global Positioning System and trilateration surveys from 1983 to 1997 on a 14-kilometer baseline across the proposed repository site for high-level radioactive waste indicate that the crust extended by 0.7 to 0.9 +/- 0.2 millimeter per year (50 to 64 +/- 14 nanostrain per year), depending on the coseismic effect of the Ms 5.4 1992 Little Skull Mountain earthquake. These strain rates are at least an order of magnitude higher than would be predicted from the Quaternary volcanic and tectonic history of the area.

Journal Article↗

PubMed1999

The mammalian gene collection.

The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources. This project will provide publicly accessible resources to the full research community. The MGC project entails the production of libraries, sequencing, and database and repository development, as well as the support of library construction, sequencing, and analytic technologies dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes.

Animals↗

PubMed2000

Influences of dietary uptake and reactive sulfides on metal bioavailability from aquatic sediments.

Understanding how animals are exposed to the large repository of metal pollutants in aquatic sediments is complicated and is important in regulatory decisions. Experiments with four types of invertebrates showed that feeding behavior and dietary uptake control bioaccumulation of cadmium, silver, nickel, and zinc. Metal concentrations in animal tissue correlated with metal concentrations extracted from sediments, but not with metal in porewater, across a range of reactive sulfide concentrations, from 0.5 to 30 micromoles per gram. These results contradict the notion that metal bioavailability in sediments is controlled by geochemical equilibration of metals between porewater and reactive sulfides, a proposed basis for regulatory criteria for metals.

Animals↗

PubMed2000

Scientific publishing. Chemists toy with the preprint future.

Last week, the giant publishing house Elsevier Science launched the first electronic archive for chemistry preprints through its ChemWeb subsidiary. The new site (preprint.chemweb.com) will be a common repository for reports on a wide range of chemistry topics and a forum for authors and readers to discuss the results. But ChemWeb could face an uphill battle in convincing authors to post their papers on the site, as many of the field's premier journals decline to accept papers that have already been posted on the Web.

Chemical Phenomena↗

PubMed1981

Geologic storage of radioactive waste: field studies in Sweden.

Access to a granitic rock mass in an iron ore mine in Sweden provided a unique opportunity for underground experiments related to the geologic disposal of radioactive waste. These field tests demonstrated the importance of hydrogeology and the difficulties in predicting the thermomechanical behavior of fractured granitic rocks. To characterize a site fully, measurements made from the surface must be supplemented by extensive subsurface measurements and experiments. Much effort is needed at this stage to generate the technology required for the development of waste repositories.

Geological Phenomena↗