Incorporation of biotin-labeled deoxyuridine triphosphate into DNA during excision repair and electron microscopic visualization of repair patches

Biotin-labeled deoxyuridine triphosphate (BiodUTP) has the potential to be a useful affinity probe for studies on DNA repair, if it can be incorporated into DNA repair patches and does not inhibit subsequent steps in the excision repair pathway. We have synthesized BiodUTP by an improved procedure and have used permeable normal human fibroblasts to determine the effect of substituting BiodUTP for thymidine triphosphate on several steps in the excision repair pathway: incision, polymerization, ligation, and nucleosome rearrangement. The results demonstrate that BiodUTP is efficiently incorporated into repair patches and has little or no effect on the repair process. The presence of BiodUMP in ligated repair patches has been used to visualize the repair patches by electron microscopy following incubation with ferritin-labeled avidin. This approach has been used to estimate the maximum size of repair patches induced by ultraviolet radiation.     

Incorporation of Na,K-ATPase into human erythrocyte membranes using liposomes

A procedure for incorporation of isolated cattle brain Na,K-ATPase into erythrocyte membranes by proteoliposomes has been elaborated. The Na,K-ATPase activity of proteoliposome-treated human erythrocytes containing incorporated Na,K-ATPase does not exceed that of control erythrocytes. In the erythrocyte membrane the incorporated enzyme exists in a functionally active state and retains the vector properties of the Na+-pump. Exogenous ATP stimulates 22Na influx and 86Rb efflux in and from the erythrocytes.     

Fusion of proteoliposomes and cells. ATP-dependent Ca2+ uptake into erythrocytes catalyzed by Ca2+-ATPase from skeletal muscle

Purified Ca2+-ATPase from rabbit skeletal muscle has been incorporated into intact erythrocyte membranes by a two-step procedure. The isolated protein was reconstituted into proteoliposomes composed of phosphatidylethanolamine, phosphatidylcholine, and cardiolipin (50:20:30%, respectively). The resulting proteoliposomes were fused with erythrocytes in presence of La3+, Ca2+, or Mg2+. Subsequently, 45Ca uptake into the cells could be demonstrated. It was dependent on externally added ATP, inhibited by N-ethylmaleimide and p-hydroxymercuribenzoate, and enhanced by inactivation of the endogenous Ca2+-ATPase which catalyzes Ca2+ extrusion from the cells. The insertion of the protein did not induce cell lysis, but the cells did become more fragile. Functional insertion of isolated membrane proteins into cell membranes allows a new approach to research of plasma membranes.     

A ganglioside spin label: ganglioside head group interactions.

A general procedure has been developed for covalent attachment of a nitroxide spin label in the head group region of gangliosides. Gangliosides so labeled and incorporated into lipid bilayer vesicles give a sharp, 3-line spectrum characteristic of a highly mobile structure. The molecular basis of apparent ganglioside-ganglioside head group interaction is briefly discussed.     

Stereoselective Nucleoside Deuteration for NMR Studies of DNA

A procedure has been elaborated for stereoselective deuterium substitution of one of the diastereotopic 5′-protons in 2′-deoxynucleotides. The synthetic scheme uses the reduction of the 5-oxosugar derivative with deuterated Alpine-Borane. The resulting deuterosugar is converted into pyrimidine nucleosides and incorporated into DNA using standard protocols. Comparison of two-dimensional NMR spectra of the fully protonated and partially deuterated duplexes allowed us to assign diastereotopic 5′ protons, increasing the number of experimental restraints used for structure determination.     

Chemical crosslinking and the stabilization of proteins and enzymes.

The technique of chemical crosslinking has been used to enhance the stability of proteins and enzymes. In this procedure, the molecule is braced with chemical crosslinks either intramolecularly or intermolecularly to another species to reinforce its active structure. Various chemicals have been used for this purpose. The bifunctional reagents are the most prominent. These compounds are derived from group-specific reagents and may be classified into homobifunctional, heterobifunctional, and zero-length crosslinkers. Different physical and chemical characteristics have been incorporated into these chemicals. Their versatility holds great potential in preparing chemically, thermally, and mechanically stable proteins and enzymes for industrial applications.     

Knowledge-based modeling of the serine protease triad into non-proteases.

The Asp-His-Ser triad of serine proteases has been regarded, in the present study, as an independent catalytic motif, because in nature it has been incorporated at the active sites of enzymes as diverse as the serine proteases and the lipases. Incorporating this motif into non-protease scaffolds, by rational design and mutagenesis, might lead to the generation of novel catalysts. As an aid to such experiments, a knowledge-based computer modeling procedure has been developed to model the protease Asp-His-Ser triad into non-proteases. Catalytic triads from a set of trypsin family proteases have been analyzed and criteria that characterize the geometry of the triads have been obtained. Using these criteria, the modeling procedure first identifies sites in non-proteases that are suitable for modeling the protease triad. H-bonded Asp-His-Ser triads, that mimic the protease catalytic triad in geometry, are then modeled in at these sites, provided it is stereochemically possible to do so. Thus non-protease sites at which H-bonded Asp-His-Ser triads are successfully modeled in may be considered for mutagenesis experiments that aim at introducing the protease triad into non-proteases. The triad modeling procedure has been used to identify sites for introducing the protease triad in three binding proteins and an immunoglobulin. A scoring function, depending on inter-residue distances, solvent accessibility and the substitution potential of amino acid residues at the modeling sites in the host proteins, has been used to assess the quality of the model triads.     

Effects of pancreatin on the growth of reovirus

Wallis, Craig (Baylor University College of Medicine, Houston, Tex.), Joseph L. Melnick, and Fred Rapp. Effects of pancreatin on the growth of reovirus. J. Bacteriol. 92:155-160. 1966.-The influence of pancreatin and other proteolytic enzymes on the growth, plaque formation, and antigenicity of reovirus was studied. Single-cycle yields of virus in the presence of enzyme were not increased, but multiple-cycle yields of virus were greatly enhanced. Immunofluorescence studies demonstrated that the transmission of reovirus from cell to cell is more rapid in the presence of the enzyme. These findings led to the development of a rapid plaque assay system for reovirus, a virus which has previously been difficult to assay by the plaque method. In the recommended procedure, pancreatin is incorporated into the agar overlay. Monkeys immunized with enzyme-treated reovirus yielded higher antibody titers than animals receiving the same amount of untreated virus.     

Bend propagation in flagella. II. Incorporation of dynein cross-bridge kinetics into the equations of motion.

The cross-bridge formalism of T. Hill has been incorporated into the nonlinear differential equations describing planar flagellar motion in an external viscous medium. A stable numerical procedure for solution of these equations is presented. A self-consistent two-state diagram with curvature-dependent rate functions is sufficient to generate stable propagating waves with frequencies and amplitudes typical of sperm flagella. For a particular choice of attachment and detachment rate functions, reasonable variation of frequency and wave speed with increasing viscosity is also obtained. The method can easily be extended to study more realistic state diagrams.     

Adding amino acids to the genetic repertoire

Considerable progress has been made in expanding the number and nature of genetically encoded amino acids in Escherichia coli, yeast and mammalian cells in the past four years. To date, over 30 unnatural amino acids have been cotranslationally incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding orthogonal tRNA-aminoacyl-tRNA synthetase pair. The incorporated amino acids contain spectroscopic probes, post-translational modifications, metal chelators, photoaffinity labels and unique functional groups. The ability to genetically encode additional amino acids, beyond the common 20, provides a powerful approach for probing protein structure and function both in vitro and in vivo, as well as generating proteins with new or enhanced properties.     

Adaptation of wastewater surface flow wetland formulae for application in constructed stormwater wetlands

Over the past 30 years, the use of constructed wetlands for wastewater treatment has been a topic of significant research culminating in a good data base from which simplistic equations have been derived to aid in the design of these facilities to meet long term water quality treatment performance criteria. Over the past decade, the use of treatment wetlands has extended to stormwater and combined sewer overflow (CSO) management applications. Designing constructed wetlands for stormwater and CSO applications have unique challenges stemming from the highly stochastic nature of the hydraulic and pollutant loading on a stormwater wetland compared with wastewater treatment systems. This paper explores the possibility of adapting the simplistic models for wastewater wetlands for interim use in developing design guidelines for stormwater wetland systems. A procedure that takes into account the unsteady intermittent nature of stormwater inflows to these wetlands has been incorporated into one of these simplistic models and a case study presented to demonstrate the application of the procedure.     

Allocation of maternal- and ejaculate-derived proteins to reproduction in female crickets, Teleogryllus oceanicus

Female fitness has traditionally been thought to be maximized with one or a few matings. More recent research suggests that polyandry, mating with two or more males, can generate an increase in the viability of offspring females produce. However, the mechanism(s) underlying enhanced offspring viability remain largely unknown. The Australian field cricket Teleogryllus oceanicus has proved a useful model for examining the evolutionary significance of polyandry. Embryo viability appears to be associated with a male's investment in accessory gland tissue, implicating a role for seminal fluid. Here, I used amino acids labelled with different radio isotopes to identify proteins manufactured by males and females before they engaged in reproduction. Males incorporated 95% of the radiolabel into the testes, accessory glands and the ejaculate that was transferred to the female at mating. Male ejaculate compounds were incorporated predominantly into the female's somatic tissue. Relatively more female compounds were incorporated into the ovaries and into laid eggs than ejaculate compounds, and relatively fewer female compounds were sequestered in the somatic tissue than ejaculate compounds. The patterns observed suggest that while ejaculate compounds may be incorporated directly into eggs, they are likely to have a larger effect on maternal allocation to offspring.     

Changes of intracellular Ca++ as measured by arsenazo III in relation to the K permeability of human erythrocyte ghosts.

A Ca-sensitive dye, arsenazo III, has been incorporated into resealed human erythrocyte ghosts and calibrated to monitor continuously micromolar concentrations of intracellular ionized Ca ([Ca++]i). When the external concentration of Ca is much greater than [Ca++]i, [Ca++]i increases because of a net balance between Ca influx and efflux. Dynamic changes in [Ca++]i regulate K efflux, which in turn may influence the rate of Ca influx. A procedure for purifying arsenazo III is also described.     

Thymidine inhibits the incorporation of 5-fluoro-2'-deoxyuridine to DNA of mouse mammary tumour.

5-Fluoro-2'-deoxyuridine is incorporated into DNA of mouse breast tumour in vivo. The incorporation is inhibited by thymidine. Part of the fluorodeoxyuridine is cleaved to fluorouracil and is incorporated into RNA. This incorporation is enhanced by thymidine. The result suggests that the major mechanism of action of the fluorouracil is due to its incorporation into RNA.     

The preparation of 5-cyanouracil and 5-cyano-2''-deoxyuridine from the corresponding 5-iodo derivative and cuprous cyanide.

5-Cyanouracil has been prepared in high yield from cuprous cyanide and 5-iodouracil. The deoxynucleoside has been similarly prepared form 5-iodo-2'-deoxyuridine and this has enabled these compounds to be labelled with (14-C) cyanide. Attempts have been made to incorporate 5-cyanouracil into Escherichia coli 15T and into Mycoplasma mycoides var. capri DNA under conditions in which several other 5-substituted uracils have been incorporated, but without success. Similarly 5-cyano-2'-deoxyuridine could not be incorporated into the DNA of T3 phage under conditions in which 5-bromo-2'-deoxyuridine is easily incorporated. These results suggest that the criteria for a 5-substituted uracil to be incorporated into DNA in vivo depends on some factor other than the size of the substituent.     

A novel method for the determination of carbonyl groups in cellulosics by fluorescence labeling. 1. Method development

A novel method to accurately determine the carbonyl content in cellulosic materials by fluorescence labeling with carbazole-9-carboxylic acid [2-(2-aminooxyethoxy)ethoxy]amide has been developed. The procedure can readily be incorporated into a gel permeation chromatography (GPC) system with refractive index and multiple-angle laser light scattering detection. Both a homogeneous procedure, working in DMAc/LiCl (2.5%, w/v), and a heterogeneous derivatization approach, using aqueous buffer pH 4.0, for determination of carbonyls in pulps have been optimized with regard to reaction conditions, presence of catalysts, reproducibility, and completeness of conversion. The homogeneous labeling requires prolonged reaction times and removal of excess marker prior to GPC analysis by a time-consuming precipitation-washing-redissolution sequence, which is not needed in the heterogeneous approach. The heterogeneous procedure offers the additional advantages of higher efficiency, shortened analysis times, increased simplicity, and widest applicability.     

New ways to admire zebrafish: progress in functional genomics research methodology

The main challenge of the post-genomic era is to functionally characterize genes identified by the genome sequencing projects. Model organisms, including zebrafish, are indispensable for this demanding task. Zebrafish has been successfully incorporated into large-scale genetic screens due to the optical clarity of the embryos and their accessibility to various experimental techniques throughout development. The attractiveness of the zebrafish as a model organism is enhanced by the availability of continuously improving genomic tools and methodologies for functional characterization of the gene. This article will highlight the current techniques used in the field, with the focus on transgenesis.     

RNA synthesis in nuclei of rat liver and of human lymphocytes.

Physico-chemical properties and RNA synthesis in the rat liver and human lymphocytes have been compared in a nuclear system in vitro. Human lymphocytes were isolated from blood of healthy donors and of chronic lymphocytic leukaemia patients. The isolated nuclei served as the source of polymerase and template DNA. 3H-CTP was incorporated into the acid insoluble fraction linearly for 60 min. The nuclei of lymphocytes contained small amounts of RNA and protein, and the isolation procedure was complicated. Rat liver nuclei seem to be less prone to clumping at high pH values and may incorporate much more 3H-CTP. The nuclear synthesis was compared with incorporation of 3H-rU and 32P-orthophosphate into nuclear RNA of intact lymphocytes. Normal cells easily incorporated 32-P, and in contrast leukaemic cells incorporated 3H-rU to a greater extent.     

Isolation of antibodies against different protein conformations using immunoaffinity chromatography

Physiological effects of DNA bases other than A, G, C, and T as well as ways of removal of such bases from genomes are studied intensely. Methods for targeted insertion of modified bases into DNA, therefore, are highly demanded in the fields of DNA repair and epigenetics. This article describes efficient procedures for incorporation of modified DNA bases into a plasmid-borne enhanced green fluorescent protein (EGFP) gene. The procedure exploits excision of a stretch of 18 nt from either the transcribed or nontranscribed DNA strand with the help of the sequence-specific nicking endonucleases Nb.Bpu10I and Nt.Bpu10I. The excised single-stranded oligonucleotide is then swapped for a synthetic DNA strand containing a desired base modification. Base modifications that form Watson-Crick-type base pairs were efficiently incorporated into plasmid DNA by a straightforward strand exchange, which was achieved by local melting in the presence of large excesses of the synthetic oligonucleotides and reannealing followed by ligation. Base modifications that cause significant distortions of the normal DNA structure, such as thymine glycol and uracil mispaired with guanine, failed to produce high yields of direct strand exchange but could still be incorporated very efficiently when the excised fragment was depleted in an intermediate step.     

Multiple peptide synthesis (Pepscan method) for the systematic analysis of B- and T-cell epitopes: Application to parasite proteins

In 1984 Mario Geysen and his colleagues described a technique for the simultaneous synthesis of hundreds of peptides on polyethylene rods. The peptides, still on the rods, could be used directly in enzyme-linked immunosorbent assays (ELISAs) and in this way linear parts of B-cell epitopes could be mapped. For the analysis of T-cell epitopes, peptides can be cleaved from the rods and incorporated into proliferation assays. This method, called the 'Pepscan' procedure, has been used for the detailed characterization of epitopes of viruses, Chlamydia and Mycobacteria: it is a powerful new approach to the epitope mapping of parasite proteins.