Genomic footprinting in mammalian cells with ultraviolet light

A simple and accurate genomic primer extension method has been developed to detect ultraviolet footprinting patterns of regulatory protein-DNA interactions in mammalian genomic DNA. The technique can also detect footprinting or sequencing patterns introduced into genomic DNA by other methods. Purified genomic DNA, containing either damaged bases or strand breaks introduced by footprinting or sequencing reactions, is first cut with a convenient restriction enzyme to reduce its molecular weight. A highly radioactive single-stranded DNA primer that is complementary to a region of genomic DNA whose sequence or footprint one wishes to examine is then mixed with 50 micrograms of restriction enzyme-cut genomic DNA. The primer is approximately 100 bases long and contains 85 radioactive phosphates, each of specific activity 3000 Ci/mmol (1 Ci = 37 GBq). A simple and fast method for preparing such primers is described. Following brief heat denaturation at 100 degrees C, the solution of genomic DNA and primer is cooled to 74 degrees C and a second solution containing Taq polymerase (Thermus aquaticus DNA polymerase) and the four deoxynucleotide triphosphates is added to initiate primer extension of genomic DNA. Taq polymerase extends genomic hybridized primer until its polymerization reaction is terminated either by a damaged base or strand break in genomic DNA or by the addition of dideoxynucleotide triphosphates in the polymerization reaction. The concurrent primer hybridization-extension reaction is terminated after 5 hr and unhybridized primer is digested away by mung bean nuclease. Primer-extended genomic DNA is then denatured and electrophoresed on a polyacrylamide sequencing gel, and radioactive primer extension products are revealed by autoradiography. By using this method we demonstrate that it is possible to footprint with ultraviolet light, in intact monkey cells, regulatory protein--DNA interactions along a single copy of a simian virus 40 viral genome integrated into the monkey genome.

Grating-encoded multichannel photorefractive incoherent-to-coherent optical conversion

A dynamic multichannel incoherent-to-coherent optical converter based on the photorefractive effect of SBN:Ce is described. A number of grating-encoded input images, illuminated by incoherent light, are projected onto the crystal to yield photoinduced phase gratings. Coherent positive replicas of these images are simultaneously reconstructed by a coherent read beam. A simple theoretical description of this converter and corresponding experimental results are presented.

B----A transitions within a 5 S ribosomal RNA gene are highly sequence-specific

The UV footprinting technique has been used to detect and map, at single nucleotide resolution, the formation of A conformations within a sea urchin 5S ribosomal RNA gene. Increasing amounts of the dehydrating agent, trifluorethanol, were used to induce the B----A transition. Our measurements argue that the B----A transition is highly sequence-specific. Fourteen different sequences within a fragment of DNA bearing the 5 S gene were found to undergo the B----A transition independently of one another. There is a striking relationship between the midpoint of the B----A transition for each stretch of DNA and its (G+C) content. DNA sequences at the boundary between A and B conformations do not appear to be significantly distorted. A (dAdT)8 tract at the 3' end of the 5 S gene undergoes the B----A transition in two cooperative steps suggesting that for some sequences the B----A transition may actually proceed through the formation of a previously unidentified intermediate. Although the sequence specificity of the B----A transition may be exploited by regulatory proteins when they bind DNA, our measurements argue that binding of the Xenopus laevis transcription factor 111A to 5 S genes does not.

Studies of the proliferation and differentiation of immature myeloid cells in vitro. I. Chronic myelogenous leukemia

Immature cells prepared from chronic myelogenous leukemic patients in the chronic or blastic phase of their disease were placed into suspension culture in vitro and studied over a 2-week period. Regardless of the status of the disease, the immature cells proliferated and maintained good viability. In contrast, evolution of the disease toward blastic crisis was associated with a progressive loss in the ability of the immature cells to differentiate. Cell proliferation and differentiation were independent of added growth factors.

Studies of the proliferation and differentiation of immature myeloid cells in vitro. II. Acute myelogenous leukemia

Immature myeloid cells prepared from patients with AML were placed into suspension culture and studied over a 2-week period. Cell numbers usually fell and viability was not well maintained. Some degree of differentiation was observed in most cultures. Considering these observations, together with those derived from parallel studies of immature CML cells, the data suggest that AML cells are more dependent than CML cells on environmental conditions for the maintenance of cell viability and proliferation. This is especially the case for AML cells obtained at the time of initial diagnosis. On the other hand, AML cells and myeloid blastic crisis CML cells are similar with respect to their apparent greater ability to differentiate in vitro than in vivo. The addition of recombinant hemopoietins to the suspension cultures of AML cells is associated with either increased proliferation or differentiation but not both. The cells of different patients respond differently to the different hemopoietins and the different hemopoietins produce different affects in cultures of cells obtained from the same patient.

Uracil-DNA glycosylase inhibitor gene of bacteriophage PBS2 encodes a binding protein specific for uracil-DNA glycosylase

The uracil-DNA glycosylase inhibitor gene (ugi) of the Bacillus subtilis bacteriophage PBS2 has been subcloned to a 720-base pair DNA fragment contained in pZW2-0.7 and its nucleotide sequence determined. Using nucleotide deletion analysis, we have located the cloned ugi gene along with potential regulatory elements. A promoter-like region (-10 and -35 consensus sequences) similar to other B. subtilis genes and the Shine-Dalgarno sequence characteristic of Gram-positive bacteria were both identified upstream from the initiator AUG codon. A 17-nucleotide exact inverted repeat followed by runs of adenine and thymine residues was positioned almost immediately downstream of the ochre codon. The ugi gene product was identified on sodium dodecyl sulfate-polyacrylamide gels using Escherichia coli minicells containing pZW2-0.7 and by recovering uracil-DNA glycosylase inhibitor activity following electrophoresis. The ugi gene codes for an acidic polypeptide of 9,477 molecular weight (84 amino acids) whose electrophoretic mobility was greater than predicted for a protein of this size. The mode of inhibition did not appear to involve a catalytic process nor did it directly involve inhibitor-DNA interaction. Rather, the inhibitor protein was shown to bind physically to the E. coli uracil-DNA glycosylase, forming a 36,000 molecular weight complex. This complex seems to be reversible, since inhibitor activity was recovered after heat treatment of the complex. In addition, we demonstrated that the inhibitor protein is active against uracil-DNA glycosylases isolated from several diverse biological sources but inactive against E. coli deoxyuridine triphosphatase, DNA polymerase I, and DNA polymerase alpha, beta, and gamma.

Normally cycling and latch bridges in venous smooth muscle

We have studied the mechanical properties of the crossbridges of canine saphenous venous smooth muscle during activation by electrical stimulation. A length-tension relationship study showed that at optimal length (1o) the maximum isometric tension (Po) developed was 87.9 mN/mm2. Resting tension at 1o was only 6% Po, which indicates a very compliant muscle. Active tension was observed at muscle lengths greater than 0.3 1o. The maximum shortening capacity was 0.65 1o. Force-velocity and series elastic characteristics were determined by the method of quick release to a set of load clamps applied during the course of an isometric contraction. The data were fitted by the hyperbolic Hill equation. Estimated maximum shortening velocity at zero load (Vo) an index of the crossbridge cycling rate) was 0.26 1o/s which was attained early in the contraction (5 s after the stimulation). A 11.9% decline in Vo was observed at the plateau of the contraction which occurred at 15 s. The stress (sigma)-strain (epsilon) curve for the series elastic component could be approximated by the equation sigma = B[exp(A epsilon)-1], where A = 76.51 (1/1o), B = 2.89 mN/mm2 at 5 s and A = 61.49 (1/1o), B = 1.85 mN/mm2 at 15 s. Like other smooth muscles, in general, saphenous vein develops considerable isometric tension and has a high shortening capacity but a low shortening velocity. The reduction in shortening velocity that occurs after 5 s in an isometric contraction is probably due to the development of so-called latch bridges.

Ticlopidine in China: comparative study on the effect of two dose levels on bleeding time and platelet function in healthy volunteers

The compared inhibitory effects of two dose levels of ticlopidine (250 and 500 mg/day) on bleeding time and platelet function in Chinese volunteers have been studied in a placebo-controlled study. Ticlopidine exerted several significant effects: namely prolongation of bleeding time, inhibition of ADP-induced platelet aggregation, reduction of the thromboxane B2 synthesis induced by collagen as well as by ADP. The daily dose of 250 mg did not show significantly different effects as compared to the western, usually recommended daily dose of 500 mg. At the daily dose of 500 mg, adverse reactions occurred more frequently than at the daily dose of 250 mg, but no serious side effects necessitating discontinuation of treatment, or abnormalities in hematological and liver function parameters were observed at these two dose levels. In Chinese people, ticlopidine therapy should be administered at a daily dose of 250 mg.

Changes in arachidonic acid metabolite patterns in alloxan-induced diabetic rats

The vasodepressor responses to intravenous injections of arachidonic acid, and the formation of its metabolites, were studied in rats made diabetic 1 or 2 weeks after a 1-dose alloxan treatment. Arachidonic acid dose-dependently decreased the diastolic blood pressure in normal animals, but this hypotensive effect was significantly weaker in 2-week postalloxan-treated rats. Indometacin abolished arachidonic-acid-induced depressor responses in both normal and diabetic animals. Hypotension induced by sodium nitroprusside was of the same magnitude in non-diabetic and insulin deficient rats. Plasma levels of thromboxane B2 were significantly increased in both the 1- and 2-week diabetic rats, being greater in the latter group; those of 6-keto-PGF1 alpha remained unchanged during the 2-week diabetic period. It is concluded that the attenuation by diabetes of depressor responses to arachidonic acid could be due to changes in the thromboxane/prostacyclin balance, with thromboxane formation being elevated whereas prostacyclin generation remains unaffected.

How rapid are the internal reactions of the ubiquinol:cytochrome c 2 oxidoreductase?

The temperature dependence of the partial reactions leading to turn-over of the UQH2:cyt c 2 oxidoreductase of Rhodobacter sphaeroides have been studied. The redox properties of the cytochrome components show a weak temperature dependence over the range 280-330 K, with coefficients of about 1 m V per degree; our results suggest that the other components show similar dependencies, so that no significant change in the gradient of standard free-energy between components occurs over this temperature range. The rates of the reactions of the high potential chain (the Rieske iron sulfur center, cytochromes c 1 and c 2, reaction center primary donor) show a weak temperature dependence, indicating an activation energy < 8 kJ per mole for electron transfer in this chain. The oxidation of ubiquinol at the Qz-site of the complex showed a strong temperature dependence, with an activation energy of about 32 kJ mole(-1). The electron transfer from cytochrome b-566 to cytochrome b-561 was not rate determining at any temperature, and did not contribute to the energy barrier. The activation energy of 32 kJ mole(-1) for quinol oxidation was the same for all states of the quinone pool (fully oxidized, partially reduced, or fully reduced before the flash). We suggest that the activation barrier is in the reaction by which ubiquinol at the catalytic site is oxidized to semiquinone. The most economical scheme for this reaction would have the semiquinone intermediate at the energy level indicated by the activation barrier. We discuss the plausibility of this simple model, and the values for rate constants, stability constant, the redox potentials of the intermediate couples, and the binding constant for the semiquinone, which are pertinent to the mechanism of the ubiquinol oxidizing site.

Immune responses in mice to different noncovalent complexes of meningococcal B polysaccharide and outer membrane proteins

Noncovalent complexes of meningococcal group B polysaccharide and outer membrane proteins (OMPs) from serotypes 2a, 2b, 6, 8, and 15 were made either by coextraction of the two components from culture supernatants or by separate preparation of both OMPs and B polysaccharide with subsequent mixing of the two components. The former method showed a markedly greater degree of binding of B polysaccharide to OMPs, a less heterogeneous composition of OMPs, and a lower lipopolysaccharide content. Immunization of mice with these complexes showed that a higher degree of binding of B polysaccharide to OMPs resulted in a higher anti-B response. Western blotting (immunoblotting) and solid-phase radioimmunoassay techniques confirmed that antibody cross-reactions occur among OMP serotypes. The occurrence of common T-cell determinants between OMP serotypes was suggested when mice primed with a type 6 OMP complex and challenged with a homologous or heterologous serotype complex responded with significantly higher anti-B titers than unprimed animals. These memory T cells persisted for at least 12 months in mice.

Assessing the risks of releasing recombinant Streptomyces in soil

Streptomyces spp. are soil microorganisms that are important in decomposition of organic matter in soil. Genetic exchange among Streptomyces species is known to occur readily both on agar and in soil in the laboratory and evidence indicates that transfer of genes from released recombinant Streptomyces to native soil streptomycetes also occurs. Minimal data are available on the environmental effects of such gene transfer.

Multibeam coupling in photorefractive SBN:Ce

Theoretical and experimental results are presented for simultaneous multibeam coupling in photorefractive SBN:Ce. Within a single crystal, multiple signals are amplified through a coupling process that employs a single pump. The coupling gain of each signal results from coupling both between the pump and the signal and between different signals. The amount of gain that each signal receives is dependent on the intensity of the incident signal; thus a competition for the gain exists among the various signals.

Differential expression of cellular oncogenes during rat liver development

The expression of a number of proto-oncogenes (myc, erb B, Ha-ras, bas, rel, mos, sis, myb, ki-ras, fms, src and fos) was studied in developing rat liver. Northern blot hybridization shows that cellular counterpart of erb B, Ha-ras, and fos oncogenes were in an early stage of liver development, and the expressions of these proto-oncogenes gradually decreased as the liver developed, while c-myc transcript was found only in the rat fetal liver. The transcripts of these oncogenes were found in high level in Morris hepatoma 7777. Bas proto-oncogene was found in high expression at early stages of rat liver development but was not in hepatoma 7777. The expression of other proto-oncogenes studied (src, fm, rel, mos, sis, myb and ki-ras) did not change significantly during liver development and was almost the same in hepatoma and normal adult liver. Southern blot analysis demonstrates that gene amplification and apparent gene rearrangement were not responsible for the change in expression of erb B, Ha-ras, myc and fos proto-oncogenes. Our study gives further evidence that erb B, myc, Ha-ras and fos proto-oncogenes are involved in the control of cell growth and in the process of rat hepatocarcinogenesis.

DNA probes for mycobacteria. I. Isolation of DNA probes for the identification of Mycobacterium tuberculosis complex and for mycobacteria other than tuberculosis (MOTT)

Traditional methods used in identifying mycobacteria such as acid-fast bacillus stains and culture are often time-consuming, insensitive and non-specific. The isolation of DNA probes, coupled to a non-radioactive, e.g. biotin-based detection system, have the potential to foster the development of clinical assays for Mycobacterium tuberculosis and mycobacteria other than tuberculosis (MOTT) that are rapid, sensitive and specific. To this end, we have isolated two different probes: one which is specific for the Mtb complex and one which recognizes all other potentially pathogenic mycobacteria. The use of these probes in combination should allow the detection and differentiation of M. tuberculosis from MOTT. To isolate the first probe, we prepared a library of M. tuberculosis DNA fragments in a lambda EMBL phage vector. Recombinant phage were screened by plaque-lift hybridization procedures using nick-translated mycobacterial genomic DNA to identify sequences specific to the Mtb complex. Inserts from candidate recombinant phage were purified, nick-translated and hybridized against a wide variety of filter-bound mycobacterial and non-mycobacterial DNAs. Two clones were identified which hybridized to the closely related M. tuberculosis, M. bovis and M. microti but not to other species of mycobacteria. The second probe was isolated by preparing a library of M. malmoense DNA fragments in lambda EMBL and screening by plaque-lift hybridization. One clone was identified which, in addition to recognizing members of the Mtb complex, also hybridized to M. intracellulare, M. malmoense, M. scrofulaceum, M. simiae, M. xenopi, M. avium, M. szulgai, M. kansasii and M. haemophilum. None of the three clones hybridized to DNA from non-mycobacterial species.

Uracil-DNA glycosylase inhibitor of bacteriophage PBS2: cloning and effects of expression of the inhibitor gene in Escherichia coli

The uracil-DNA glycosylase inhibitor gene of bacteriophage PBS2 was cloned, and the effects of this inhibitor on Escherichia coli cells that contain uracil-DNA glycosylase activity were determined. A PBS2 genomic library was constructed by inserting EcoRI restriction fragments of PBS2 DNA into a plasmid pUC19 vector. The library was used to transform wild-type (ung+) E. coli, and the presence of the functional inhibitor gene was determined by screening for colonies that supported growth of M13mp19 phage containing uracil-DNA. A clone was identified that carried a 4.1-kilobase EcoRI DNA insert in the vector plasmid. Extracts of cells transformed with this recombinant plasmid lacked detectable uracil-DNA glycosylase activity and contained a protein that inhibited the activity of purified E. coli uracil-DNA glycosylase in vitro. The uracil-DNA glycosylase inhibitor expressed in these E. coli was partially purified and characterized as a heat-stable protein with a native molecular weight of about 18,000. Hence, we conclude that the PBS2 uracil-DNA glycosylase inhibitor gene was cloned and that the gene product has properties similar to those from PBS2-infected Bacillus subtilis cells. Inhibitor gene expression in E. coli resulted in (i) a weak mutator phenotype, (ii) a growth rate similar to that of E. coli containing pUC19 alone, (iii) a sensitivity to the antifolate drug aminopterin similar to that of cells lacking the inhibitor gene, and (iv) an increased resistance to the lethal effects of 5-fluoro-2'-deoxyuridine. These physiological properties are consistent with the phenotypes of other ung mutants.

Selective visualization of gene structure with ultraviolet light

The ability of the ultraviolet (UV) "footprinting" technique to detect chromatin has been investigated in vitro. Two basic types of chromatin, a phased nucleosome and a phased nucleosome containing a phased H1 protein, have been reconstituted onto a cloned 5S ribosomal RNA gene from sea urchin. The histone-DNA interactions in each complex have been probed with exonuclease III, DNase I, dimethyl sulfate, and UV light. Whereas DNase I and exonuclease III readily detect interactions between histones and DNA, UV light and dimethyl sulfate do not. In contrast to histone-DNA interactions, we demonstrate that intimate sequence-specific contacts between the same sea urchin 5S DNA and the Xenopus laevis transcription factor IIIA (TFIIIA) are readily detected with UV light. Since the sensitivity of UV light for TFIIIA contacts is similar to its sensitivity for other regulatory protein-DNA contacts, these studies demonstrate the feasibility of using UV light to selectively visualize regulatory protein-DNA interactions in vivo with little or no interference from histone-DNA interactions.

Successful replantation in ten-digit complete amputations

The authors report a case of successful replantation of all fingers in a ten-finger complete amputation. Among the factors responsible for the successful outcome were an adequate number of microsurgically-trained resident surgeons and staff, good organization and supervision by senior staff, emphasis on precision and perseverance in the operative procedures, and postoperative management. Follow-up is 15 months, and the patient now has a pair of functionally and cosmetically good hands.

Telomeric association: another characteristic of cancer chromosomes?

Telomeric associations between single chromatids and double chromatids of nonhomologous normal human chromosomes and altered markers were observed in two morphologically distinct squamous-cell carcinoma lines derived from a surgical specimen. Chromosomes 2, 3, 5, and 16 were associated by their telomeric ends more frequently than other chromosomes.

Molecular cloning of a species-specific DNA probe for Campylobacter jejuni

Conventional procedures for isolating and identifying Campylobacter jejuni are cumbersome and time-consuming. A simpler approach would be to use DNA probes to identify these organisms. To obtain such probes we cloned chromosomal DNA from C. jejuni into the lambda replacement vector EMBL 4. Recombinant phages were screened for C. jejuni-specific inserts by DNA hybridization using chromosomal DNA from either C. jejuni or C. coli which had been radioactively labelled with 32P. By this means, recombinant phages were identified which hybridized to C. jejuni but not to C. coli DNA. These phages were then subjected to further screening using DNA from other Campylobacter species. Three DNA fragments were identified which hybridized to DNA from eight ATCC (American Type Culture Collection) strains of C. jejuni but not to DNA from C. coli, C. laridis, C. fetus or a variety of other bacterial species. These DNA fragments are suitable for use as specific probes in DNA-based diagnostic tests for C. jejuni infections.