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High-throughput assays of phagocytosis, phagosome maturation, and bacterial invasion.

Ingestion of foreign particles by macrophages and neutrophils and the fate of the vacuole that contains the ingested material are generally monitored by optical microscopy. Invasion of host cells by pathogenic bacteria and their intracellular proliferation are similarly studied by microscopy or by plating assays. These labor-intensive and time-consuming methods limit the number of assays that can be performed. The effort required to test multiple reagents or conditions can be prohibitive. We describe high-throughput assays of phagocytosis and of phagosomal maturation. An automated fluorescence microscope-based platform and associated analysis software were used to study Fcgamma receptor-mediated phagocytosis of IgG-opsonized particles by cultured murine macrophages. Phagosomal acidification was measured as an index of maturation. The same platform was similarly used to implement high-throughput assays of invasion of mammalian cells by pathogenic bacteria. The invasion of HeLa cells by Salmonella and the subsequent intracellular proliferation of the bacteria were measured rapidly and reliably in large populations of cells. These high-throughput methods are ideally suited for the efficient screening of chemical libraries to select potential drugs and of small interference RNA libraries to identify essential molecules involved in critical steps of the immune response.

Animals↗

Molecular biology and evolution of the grass endophytes.

Acremonium coenophialum Morgan-Jones et W. Gams is a maternally transmitted fungal symbiont (endophyte) of the important forage grass Festuca arundinacea Schreb. (tall fescue), and provides biological protection and enhanced fitness to its host, but its anti-mammalian ergot alkaloids detract from the usefulness of tall fescue as forage for livestock. Molecular genetic techniques and materials are being developed in order to specifically eliminate the gene(s) encoding the first enzyme in ergot alkaloid biosynthesis. These techniques will also facilitate basic studies, such as host-fungus compatibility or biosynthesis of insecticidal alkaloids. Molecular phylogenetics indicate that endophytes related to A. coenophialum have evolved on multiple occasions from strains of Epichloë typhina (Ascomycotina, Clavicipitaceae), for which the sexual cycle is known. These studies also reveal significant diversity among seedborne endophytes in individual grass species. Thus, the endophytes are an important source of biochemical potential and genetic diversity in grass-fungus symbiota.

Acremonium↗

EILATox-Oregon Workshop: blind study evaluation of Vitotox test with genotoxic and cytotoxic sample library.

In order to assess the robustness, sensitivity and specificity of a recently developed Vitotox test, 17 blind coded chemicals and three environmental water samples were tested at the EILATox-Oregon Workshop using the Thermo Electron Vitotox kit. The Vitotox test is a rapid geno- and cytotoxicity test using standard 96- or 384-well microtitre plates. The genotoxicity test is based on two genetically modified Salmonella typhimurium strains containing bacterial luciferase operon from Vibrio fisheri under the SOS inducible promoter. The SOS system is an inducible network in Escherichia coli that responds to DNA damage and activates DNA repair. The Vitotox genotoxicity test bacteria strain carries bacterial luciferase genes under the control of SOS inducible promoter and therefore any DNA damage inside the cells induces the production of bacterial luciferase. The luciferase expression is then followed with a microtitre plate luminometer for 3 h after mixing different dilutions of sample with the test bacteria. The genotoxicity index is calculated for each dilution and the genotoxicity of the sample is interpreted based on kinetic time curves and genotoxicity vs concentration/dilution curves. Cytotoxicity of the sample is determined simultaneously with another test strain containing the same luciferase operon controlled by the constitutive promoter. This bacterium produces constant bioluminescence and any decrease of the bioluminescence production is used as a marker for cytotoxicity. As a miniaturized microtitre plate assay the Vitotox test requires a very small quantity of the sample material. The samples used in the workshop were diluted 1 : 10 or 1 : 100 before testing. Genotoxicity and cytotoxicity data were collected at dilutions of 1 : 10-1 : 2000. When the samples of the EILATox-Oregon Workshop were tested using the Vitotox test, four coded chemicals out of 17 were determined to be genotoxic. Seven chemicals and one environmental sample were found to be cytotoxic. Three chemical samples were found to be both geno- and cytotoxic.

Aliivibrio fischeri↗

Conformationally constrained analogues of diacylglycerol. 21. A solid-phase method of synthesis of diacylglycerol lactones as a prelude to a combinatorial approach for the synthesis of protein kinase C isozyme-specific ligands.

A solid-phase method for the synthesis of diacylglycerol lactones as protein kinase C ligands was developed, and a small array of nine compounds were selected with the idea of testing this methodology and forecasting the reliability of the biological data as a preamble for the construction of large chemical libraries to be synthesized under the same conditions. The process started with the loading of 5-(hydroxymethyl)-5-[(4-methoxyphenoxy)methyl]-3,4,5-trihydrofuran-2-one (1) to a 3,4-dihydro-2H-pyran resin packed inside IRORI MacroKan reactors. The elements of diversity were introduced at the alpha-alkylidene (R(1)) and acyl (R(2)) positions using a set of three different aldehydes and three different acid chlorides, respectively. An LDA-mediated aldol condensation with R(1)CHO in the presence of ZnCl(2) followed by a DBU-catalyzed elimination of the triflate of the resulting aldol gave the alpha-alkylidene intermediates as mixtures of geometric isomers. Removal of the aryl-protecting group followed by acylation with R(2)COCl introduced the second element of diversity. Acid-assisted cleavage of the compounds from the resin afforded the final targets. The biological results obtained using the crude samples directly obtained from the resin compared well with those from pure materials, as the K(i) values between the two sets varied only by a factor between 1.5 and 3.7.

Binding, Competitive↗

Selection of information resources for education in medical pharmacology.

Pharmacology is the foundation science of medical pharmacotherapy. Education in medical pharmacology (EP) requires the use of information resources (IR) to meet the challenge of the continuous introduction of new drugs and new educational, didactic and pedagogical theories to enhance knowledge. Hence criteria for selecting bibliographic material for EP should be clearly outlined and implemented. In this work we present a method to select IR for EP based on systems theory and focusing on the factors determining: (a) the integration of a list of recommended IR for EP; (b) the design of the acquisition list for faculty and students work; (c) the overall organization of the resources available for its optimal use and benefit in the educational process; and (d) a general strategy for assessing the impact of the bibliographic infrastructure. The proposal is based on information from: (i) lists of recommended readings in the academic program of the Pharmacology course given at the School of Medicine of UNAM in the last 30 years; (ii) the extent of discipline development measured by two indexes derived from the contents of Goodman and Gilman's "Pharmacological Basis of Therapeutics" (G & G); (iii) the number of texts currently found in the collection of FM-UNAM which are classified in the section of Pharmacology using the Library of Congress Classification System (LCCS); and (iv) the comparison of academic versus standardized classification of pharmacology topics, such as Medical Subject Heading (MESH) and LCCS The importance of this proposal relates to its usefulness for EP and for other medical disciplines.

Books↗

Individualized human scFv vaccines produced in plants: humoral anti-idiotype responses in vaccinated mice confirm relevance to the tumor Ig.

We have developed a method for rapidly producing in plants the idiotype regions of the tumor-specific Ig as single-chain Fv (scFv) proteins for use in the treatment of non-Hodgkin's lymphoma. Variable region gene sequences were generated from either a tumor hybridoma or human tumor biopsy cells, and idiotype domains were joined by a novel linker and cloned into a modified tobacco mosaic virus (TMV) vector designed to secrete the scFv protein in infected Nicotiana benthamiana plants. Thirty-eight out of 44 human scFv proteins showed Coomassie visible material in crude secretory (interstitial fluid, IF) extracts, 21 of those between 100 and 800 microg/ml. Eight of these proteins were tested for appropriate idiotype responses in vaccinated mice. In all eight cases, anti-idiotype immune responses were induced with minimal cross reactivity to irrelevant Ig or scFv proteins. Four out of four anti-scFv sera were also shown to recognize the Ig on human tumor cells by flow cytometry analysis.

Animals↗

Forensic analysis of architectural finishes using fourier transform infrared and Raman spectroscopy, part I: the resin bases.

The ability of Raman spectroscopy and Fourier transform infrared (FT-IR) microscopy to discriminate between resins used for the manufacture of architectural finishes was examined in a study of 39 samples taken from a commercial resin library. Both Raman and FT-IR were able to discriminate between different types of resin and both split the samples into several groups (six for FT-IR, six for Raman), each of which gave similar, but not identical, spectra. In addition, three resins gave unique Raman spectra (four in FT-IR). However, approximately half the library comprised samples that were sufficiently similar that they fell into a single large group, whether classified using FT-IR or Raman, although the remaining samples fell into much smaller groups. Further sub-division of the FT-IR groups was not possible because the experimental uncertainty was of similar magnitude to the within-group variation. In contrast, Raman spectroscopy was able to further discriminate between resins that fell within the same groups because the differences in the relative band intensities of the resins, although small, were larger than the experimental uncertainty.

Architecture↗

Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA.

A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA. Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens. To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E. coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target. From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM. Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides. Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.

Aminoglycosides↗

Authorship outlets of academic health sciences librarians.

Journal articles are the most common publication format for U.S. academic health sciences librarians. This is consistent with the findings of other researchers. Of the total publications in this study, 68% were in journals. Watson found that 69% of the academic librarians' publications were published in some type of journal [8]. Similarly, Yerkey and Glogowski found that 67% of the publications in their study were journal articles, although their population consisted of all types of authors of library/information science materials [9]. Both the present study and Watson found that monographs were the second most common publication outlet. Watson found that 16% of the total publications were monographs; the current study identified 14.8% of the total publications as monographs [10]. Although Watson's findings are similar to the newer results, it is important to note that Watson's study was conducted in a different manner and included book reviews, which were not counted in the present study. The health sciences librarians in the present study published more than two thirds of their articles in library/information science journals and 27% in health sciences journals. Similarly, in Yerkey and Glogowski's study, the second-largest number of library/information science articles appeared in medical and health sciences journals [11]. Fang also found that 22.57% of the journal articles on health sciences librarianship or by health sciences librarians were in medical journals [12. This seems to demonstrate the desire of health sciences librarians to communicate with the health professionals. Yerkey and Glogowski that library and information science is an interdisciplinary field, "borrowing and supplying information to and from other disciplines"[13].

Authorship↗

Molecular cloning and functional expression of contortrostatin, a homodimeric disintegrin from southern copperhead snake venom.

Contortrostatin is a unique dimeric disintegrin isolated from southern copperhead snake venom. Through antagonism of integrins alphaIIbbeta3, alpha5beta1, alphavbeta3, and alphavbeta5, contortrostatin inhibits platelet aggregation and disrupts cancer cell adhesion and invasion. We cloned cDNA from a library made from the venom gland cells of Agkistrodon contortrix contortrix using polymerase chain reaction. We found that the contortrostatin gene is part of a precursor composed of proprotein, metalloproteinase, and disintegrin domains. The precursor cDNA is 2027 bp with a 1449-bp open reading frame. The disintegrin domain is 195 bp encoding 65 amino acids. Like other members of the disintegrin family, each subunit of contortrostatin has an RGD site, and the cysteine alignment is conserved. The disintegrin domain of the cDNA has been expressed in a eukaryotic expression system as a homodimeric fusion protein with an immunoglobulin. The recombinant protein is recognized by an antiserum against native contortrostatin in Western blot. Both the native and recombinant proteins bind to integrins alphavbeta3 and alphavbeta5. Like native contortrostatin, the recombinant fusion protein inhibits platelet aggregation, blocks cancer cell adhesion to fibronectin and vitronectin, and prevents invasion of cancer cells through a Matrigel barrier. The success of functional expression not only validates the cDNA cloning of this disintegrin, but also provides adequate material for functional studies of contortrostatin.

Agkistrodon↗

Applicability of imaging time-of flight secondary ion MS to the characterization of solid-phase synthesized combinatorial libraries.

We employ imaging time-of-flight secondary ion mass spectrometry to perform high-throughput analysis of solid-phase synthesized combinatorial libraries by acquiring mass spectra from arrays of polymer resin particles. To generalize this procedure to various types of resins and their associated chemical linkers, it is necessary to understand the dynamics associated with the analyte molecules during chemical pretreatment steps. Using stearic acid as a model compound, we examine the influence of three classes of linkers-acid or base labile linkers, a thermally labile linker, and a photochemically cleavable linker- all of which are used to anchor one end of the analyte to the polymer resin. With data obtained using secondary ion mass spectrometry, scanning electron microscopy, and X-ray photoelectron spectroscopy, we conclude that an effective treatment of the resin needs to include cleaving the linker and extracting the unbound analyte to the resin surface. We also demonstrate that the hydrophilicity of the polymeric constituents of a resin particle affects the experiments by changing the location of the analyte molecules during resin treatment. With this information, it is possible to utilize imaging TOF-SIMS to assay a range of material supports with assurance that high-quality spectra can be acquired.

Combinatorial Chemistry Techniques↗

A stereodivergent, two-directional synthesis of stereoisomeric C-linked disaccharide mimetics.

Dipyranones, such as 1,2-bis[(2R,3S,6S)-3-hydroxy-6-methoxy-3-oxo-6H-pyran-2-yl]ethane, were exploited as templates for the synthesis of some novel C-linked disaccharide analogues. Efficient methods, such as stereoselective reduction and dihydroxylation, were developed for two-directional functionalisation of these templates. Peracetylated derivatives of ten stereoisomeric disaccharide analogues [acetic acid 4,5-diacetoxy-6-methoxy-[(3',4',5'-triacetoxy-6'-methoxytetrahydropyran- 2'-yl)ethyl]tetrahydropyran-3-yl esters] were synthesised from a virtual library of 136 compounds; furthermore, an additional eight stereoisomers could have been synthesised simply by using the enantiomeric ligand in the enantioselective step. The ability of (2S,3S,4R,5R,6R)-6-methoxy-2-[2'-((2'R,3'R,4'S, 5'R,6'S)-3',4',5'-trihydroxy-6'-methoxytetrahydropyran-2'-yl) ethyl]tetrahydropyran-3,4,5-triol to bind to the repressor protein, LacI, was estimated to be similar to that of isopropyl-beta-thiogalactoside. The disaccharide mimetics were concluded to be a new and interesting class of C-linked disaccharide mimetics with promising, though largely unstudied, biological activity.

Bacterial Proteins↗

KWIC. IS IT QUICK?

In recent months several widely circulated publications have exploited the concept of key-word-in-context (KWIC) indexing. Indexes prepared through KWIC techniques are based entirely on the permuted titles of material to be analyzed and are produced at high speed with the aid of electronic computers. KWIC indexes appear to have been received with approval by scientists, whereas many librarians regard them with misgivings and are concerned about the discontinuance of certain earlier conventional subject indexes. This paper presents some of the difficulties encountered by reference librarians who have used KWIC indexes in the course of their work. A simple exercise is described which tests the speed with which a KWIC and two other indexes lead to the solution of selected reference problems. KWIC proved to be a tool which led quickly to the desired information.

Abstracting and Indexing↗

Molecular markers from the transcribed/expressed region of the genome in higher plants.

In recent years, molecular marker technology in higher plants has witnessed a shift from the so-called random DNA markers (RDMs), developed in the past arbitrarily from genomic DNA and cDNA, to the molecular markers representing the transcriptome and the other coding sequences. These markers have been described as gene targeted markers (GTMs). Another specific class of markers includes the so-called functional markers (FMs), which are supposed to have a cause and effect relationship with the traits of interest. In this review, we first describe the development of these markers representing the transcriptome or genes per se; we then discuss the uses of these markers in some detail and finally add a note on the future directions of research and the implications of the wider application of these markers in crop improvement programmes. Using suitable examples, we describe markers of different classes derived from cDNA clones, expressed sequence tags (ESTs), gene sequences and the unique (coding) sequences obtained through methyl filtration or genome normalization (high C(0) t fraction) from gDNA libraries. While we briefly describe RFLPs, SSRs, AFLPs and SNPs developed from the transcriptome (cDNA clones and EST databases), we have discussed in more detail some of the novel markers developed from the transcriptome and specific genes. These novel markers include expressed sequence tag polymorphisms (ESTPs), conserved orthologue set (COS) markers, amplified consensus genetic markers (ACGMs), gene specific tags (GSTs), resistance gene analogues (RGAs) and exon-retrotransposon amplification polymorphism (ERAP). Uses of these markers have been discussed in some detail under the following headings: development of transcript and functional maps, estimations of genetic diversity, marker-assisted selection (MAS), candidate-gene (CG) approach and map-based cloning, genetical genomics and identification of eQTLs, study of genome organization and taxonomic and phylogenetic studies. At the end, we also append a list of websites relevant to further studies on the transcriptome. For want of space, considerable information including voluminous data in the form of 12 tables, and a long list of references cited in these tables, has been placed on the Internet as electronic supplementary material (ESM), which the readers may find useful.

Chromosome Mapping↗

Affinity purification of von Willebrand factor using ligands derived from peptide libraries.

The chromatographic purification of vWF (von Willebrand Factor) from human plasma represents a challenge because it consists of multimers with molecular weights ranging from 0.5 to 10 million Daltons. Phage peptide library screening yielded a lead peptide (RLRSFY) that interacts with vWF. Conservative substitutions of terminal residues of the lead peptide led to a second peptide, RVRSFY, which was more efficient in the affinity chromatographic purification of vWF from protein mixtures. Adsorption isotherm measurements indicated multiple interactions between vWF and the immobilized peptide RVRSFY. Increases in peptide density on the chromatographic supports resulted in stronger association constants and higher maximum protein binding capacities. When the peptide density was lower than 32 mg/mL, there was no measurable interaction between vWF and immobilized peptide RVRSFY in HEPES buffer containing 0.5 M NaCl at pH 7. An increase in peptide density from 32 to 60 mg/mL increased the association constants from 0.9 x 10(6) to 2 x 10(6) (M-1). Divalent salts (calcium and magnesium chloride) were used to elute the retained vWF with 82.5% of the activity recovered. The interactions between vWF and the immobilized peptide RVRSFY are dominated by ionic attractions and also involve hydrophobic interactions at close contact. Finally, the purification of vWF from crude material PEG filtrate of a cryoprecipitate of human plasma is demonstrated using affinity chromatography with immobilized N-acetyl-RVRSFYK.

Adsorption↗

Onchocerca antigens in protection, diagnosis and pathology.

Characterization of the immune response to Onchocerca volvulus is important for the diagnosis, control and understanding of the disease it causes. The antibody response to surface, secreted and somatic antigens of the worm has therefore been examined at an individual immunoglobulin (Ig) class level, by using a panel of different human sera. Onchocerca-specific antigens tend to be of low molecular mass and preferentially recognized by IgG4 and IgE. There is considerable cross-reaction between O. volvulus and O. gibsoni, so that the latter may be an alternative source of material for use in diagnosis. A surface-enriched fraction of low molecular mass appears to be a most promising diagnostic tool. Amongst somatic antigens, two were uniquely recognized by IgG3 antibodies in sera from sowda patients, thereby providing a molecular correlate for a recognized pathological condition. Improved diagnosis is needed for detecting infection in both humans and the vector. Our target for detection in humans is a continuously released, nonimmunogenic product, which is ideally stage and parasite specific. The excretions of adult worms do contain components not recognized by antibodies in infected serum, but we cannot rule out that these are of host, rather than parasite origin. Excretions of Litomosoides carinii contain both host and parasite molecules and, in addition, stage-specific and sex-specific components. Unfortunately, however, the rate of production of excretions varies during the life of L. carinii. This finding may be relevant to the detection of Onchocerca excretions if they are produced at a similarly uneven rate. Finally, for detecting infective larvae in the vectors, we are currently screening a genomic library of O. volvulus for an appropriate probe. To date, one DNA sequence has been cloned that shows promising specificity.

Animals↗

Identification of a yeast artificial chromosome (YAC) spanning the synovial sarcoma-specific t(X;18)(p11.2;q11.2) breakpoint.

A somatic cell hybrid containing the synovial sarcoma-associated t(X;18)(p11.2;q11.2) derivative (der(X)) chromosome was used to characterize the translocation breakpoint region on the X chromosome. By using Southern hybridization of DNA from this der(X) hybrid in conjunction with Xp-region specific radiation reduced cell hybrids and probes, it was found that this breakpoint maps within the ornithine aminotransferase (OAT) L1 cluster. A yeast artificial chromosome (YAC) clone (OAT YAC2) which hybridizes to a human OAT cDNA probe and is known to contain part of the OATL1 cluster was selected and used to confirm these results both by fluorescence in situ hybridization on synovial sarcoma patient material and by hybridization of its end-clones to the der(X) containing hybrid cells. It was found that indeed the human Xp sequences contained within this YAC are split as a consequence of the (X;18) translocation. Therefore, we conclude that OAT YAC2 spans the synovial sarcoma-specific translocation breakpoint and, as such, may serve as an ideal starting point from which the gene(s) involved in the development of this soft tissue tumor can be isolated.

Animals↗

Protein-imprinted polymer with immobilized assistant recognition polymer chains.

Here we introduce a new method for preparing a protein-imprinted polymer with immobilized assistant recognition polymer chains as an additional element of monomer to create effective recognition sites. In this work the bovine serum albumin was used as template and the template protein was selectively assembled with immobilized assistant recognition polymer chains from their library, numerous limited length polymer chains with randomly distributed recognition sites and immobilizing sites. These assemblies of protein and immobilized assistant recognition polymer chains would be adsorbed by the macro porous adsorbent spheres and immobilized by cross-linking polymerization. After removing the template, binding sites that were complementary to the target protein in size, shape and position of recognition groups were exposed, and their confirmation was preserved by the cross-linked structure. The synthesized imprinted polymer was used to adsorb BSA from protein mixtures, and showed a high selectivity.

Biocompatible Materials↗