1H-NMR study of the OR1 operon in bacteriophage lambda. I. Assignment of signals from imino protons and adenine C2 protons

An oligodeoxyribonucleotide composed of 17 residues, d(TATCACCGCCAGAGGTA), and a complementary chain were synthesized. Their duplex was identical with the operator OR1, the binding site for bacteriophage lambda cro and c1 repressors. The 1H NMR spectra (500 MHz) of the duplex imino and aromatic protons were studied at 10, 20 and 25 degrees C. Signals from the imino protons of complementary base pairs and from the C2 protons of adenine (with the exception of the duplex terminal nucleotides) were assigned using the NOE technique and the known characteristics of short DNA fragment melting. No signals from the imino protons of the terminal base pairs were detected even at 10 degrees C due to fraying which increased as the temperature was raised. The assignment of signals can be used to identify centers of interaction between the operator OR1 and repressors, as well as to study possible local changes in DNA geometry.     

Anisotropic rotational motions of poly(L-glutamic acid) in the alpha-helix conformation

The anisotropic rotational motion of the backbone and the side chains of poly(L -glutamic acid) in the α-helical structure was investigated using the ¹³C-T₁ and T₂ relaxation times of all carbon atoms with directly attached protons, obtained at a ¹³C-Larmor frequency of 67.89 MHz. The evaluation of the nmr data was carried out according to the previously derived anisotropic diffusion model, in which the macromolecule is considered a rigid rod. The rotation of the backbone is characterized by two diffusion constants, D₁ and D₃, describing the rotation perpendicular to and around the symmetry axis. The additional internal motion of the C^β-methylene group is described as a jump process with a jump rate, k₁, between two allowed rotametric states. Steric considerations indicate that the occupation of the third rotameric position is forbidden. The rotation of the C^γ-methylene group is decribed as a one-dimensional diffusion process around the C^β–C^γ bond. Investigation of the temperature dependence of the relaxation parameters led to the temperature dependence of the dynamic parameters. Activation energies were determined from these data. The dynamic parameters obtained for poly(L -glutamic acid) at 291 K are compared with the corresponding results of a previous study of poly(L -lysine). The development of an anisotropic diffusion model for the motions of the rod-shaped poly(L -lysine) α-helix and its application to the interpretation of the ¹³C-relaxation data of this molecule have already been published previously. In this model, both the overall molecular tumbling and the various internal motions have been characterized by diffusion constants or jump rates typical for each process. These dynamic parameters can be calculated from the spin–lattice relaxation times, the spin–spin relaxation times and the NOE factors of the C^α, C^β, and C^γ nuclei of the polypetide. In the present paper, we describe the application of the above-mentioned dynamic model to the interpretation of ¹³C-relaxation studies of a further homopolypeptide, poly(L -glutamic acid), in the α-helical structure. Furthermore, we studied the temperature dependence of the relaxation times of this polymer and determined the anisotropic diffusion parameters at each temperature. From their temperature dependence and from comparison of our present results with the data of our previous study of poly(L -lysine), we were able to derive new insights into the intramolecular diffusion processes and the excitation of various motions.     

Radioimmunoassay for human type VI collagen and its application to tissue and body fluids

A liquid phase radioimmunoassay (RIA) was developed for pepsin-solubilized human type VI collagen, allowing quantitative analysis of this protein down to a concentration of 3 ng/ml. No cross-reactivity was observed with human collagens type I, III, IV (triple helical portion and 7-S domain), and V, nor with laminin fragment Pl and plasma fibronectin. Significant amounts of closely related antigenic material were detected in serum, bile, ascites, and mesenchymal cell culture media. Type VI collagen could be completely solubilized from several tissues by a repeated pepsin digest, and its content as determined by RIA was found to be less than 0.1% of total collagen (55-70 micrograms/g protein). In fibrotic liver tissue type VI collagen was elevated up to 10-fold (620 micrograms/g protein) when compared to normal liver. Sera of patients with fibrotic liver disease, however, revealed antigen levels usually below the narrow normal range of 22 +/- 7.8 ng/ml (mean +/- 2.5 SD). We conclude that, although type VI collagen represents a minor fraction of the interstitial collagens, its comparatively high serum levels point to a considerable turnover in the normal individual. Our data suggest that in fibrosis as exemplified in fibrotic liver disease, the metabolism of this collagen is down-regulated, while at the same time, it accumulates in the interstitial matrix.     

Nucleotide sequence analysis of a variant human T-cell leukemia virus (HTLV-Ib) provirus with a deletion in pX-I.

A variant of human T-cell leukemia virus subgroup I (HTLV-I), designated HTLV-Ib, has been isolated from a transformed T-lymphocytic cell line established from a Zairian patient with adult T-cell lymphoma. A recombinant phage clone of the variant provirus, denoted lambda MC-1, hybridizes under high stringency to HTLV-I DNA probes, but 17 of 43 restriction enzyme sites differ from those of HTLV-I, 10 of them clustering within 1.5 kilobases in the env-pX region. Since this variant virus retains its capacity to transform T-cells in vitro, and since a pX product is suspected to be important in transformation, we have determined the nucleotide sequence of the entire pX region of this virus for comparison to the prototype HTLV-I. In addition, the region between the gag and pol genes, parts of the pol and env genes, and a portion of the U3 region of the long terminal repeat sequence were also analyzed. We noted 141 single-base-pair changes among 3,897 base pairs, which were relatively well distributed over those portions of the provirus that were examined. In addition, an 11-base-pair deletion was found which included the potential initiator ATG codon of the first open reading frame of pX (pX-I). The next potential initiator codon predicted by the sequence is followed by 10 codons and then a termination codon. An identical deletion was also demonstrated in the only provirus present in another cell line established from the same patient on a different occasion after transformation in vitro of normal human umbilical cord blood cells. These results indicate that pX-I is not required for transformation.     

1H NMR study of the interaction of bacteriophage λ Cro protein with the O R 3 operator

The 17 base pair operator O _R ³ oligonucleotide, which is the preferential binding site for the Cro repressor of phage , was studied by two-dimensional NMR spectroscopy. A sequential assignment procedure based on two-dimensional Nuclear Overhauser Effect (NOESY) and scalar coupling correlated (COSY) NMR spectroscopy, together with the knowledge of the oligodesoxynucleotide sequence, made it possible to assign the non-exhangeable base protons and the H1 and the H2-H2 sugar protons of the O _R ³ operator DNA. The pattern of the observed NOE connectivities is consistent with a right-handed helical DNA structure. The base and sugar proton assignments provide the necessary information for further studies of the O _R ³ operator — Cro repressor interaction.Abbreviations COSY correlated spectroscopy - FID free induction decay - NOE nuclear Overhauser effect - NOESY nuclear Overhauser effect spectroscopy - RD relaxation delay - TSP sodium 3-trimethylsilyl-(2,2,3,3-²H₄)propionate - EDTA sodium ethylendiamine tetraacetate     

Noninvasive thermometry using multiple-frequency-band radiometry: a feasibility study

The potential use of multiple-frequency-band radiometry as a means of noninvasive sensing of one-dimensional temperature profiles is presented in this communication. The radiative energy transfer equation is solved numerically. Ideal-condition thermal noise spectra and distributions of received energy, associated with specific temperature-depth profiles, are presented. Performance characteristics are discussed.     

Prostaglandin synthesis by cells comprising the calf pulmonary artery

Prostaglandin (PG) production was evaluated in the three cell types (endothelial, smooth muscle, and fibroblast) comprising the bovine pulmonary artery. Prostacyclin (PGI2) was the predominant prostaglandin (PG) produced by endothelial, smooth muscle, and fibroblast cells as they exist in culture or in freshly excised tissue fragments. In addition to PGI2, measurable amounts of PGE2, PGF2a, and thromboxane A2 (TXA2) were also produced by these cells. Endothelial cells were the most active producers of PGs. However, the type of PG produced was characteristic of the particular cell type, while the level of production was dependent on external factors. Prostaglandin production by cultured cells, both under basal conditions and in response to stimulatory agents, was quite similar to that of the respective freshly excised tissue fragments containing a given cell type. These cells in culture could be stimulated to produce PGI2 by both angiotensin and bradykinin at very low (physiological) concentrations, a further indication of the retention of the physiological responsiveness of these cells in culture. Endothelial cells and fibroblasts were activated by bradykinin at concentrations as low as 10(-12) M but did not respond to angiotensin. Smooth muscle cells in primary and first passage cultures were activated by both bradykinin and angiotensin at 10(-12) M concentrations. Serial subcultivations of smooth muscle cells resulted in a progressive loss in their responsiveness to bradykinin stimulation. The state of cell growth proved to be an important determinant of PG production. Actively growing cells in culture synthesized less PG when compared to cells which had entered into a "quiescent" nongrowth state.     

Effect of ozone on breathing in dogs: vagal and nonvagal mechanisms

We exposed two awake dogs with a chronic tracheostomy and the cervical vagus nerves exteriorized in skin loops to 1.0 ppm of ozone (O3) for 2 h at intervals of 4 wk. We measured ventilatory variables before and after O3 exposure during rest and exercise before and after vagal block. We compared the effects of vagal blockade, exercise, and O3 on the primary determinants of breathing pattern (VT/TI, VT/TE, TI, and TE) in each of three conditions: base line (steady state), during hypercapnia, and after inhalation of 1% histamine. Under base-line conditions, O3 increased respiratory rate and decreased tidal volume (VT) by shortening time of expiration (TE) and time of inspiration (TI) without affecting VT/TI, an indicator of the neural drive to breathing. During progressive hypercapnia, O3 shortened TE and TI by effects both on tonic (nonvolume-related) and on phasic (volume-related) vagal inputs, and only the latter were prevented completely by cooling of the vagus nerves. Histamine-induced tachypnea was increased by O3 and was totally blocked by cooling the vagus nerves. We conclude that O3 shortens the timing of respiration without increasing ventilatory drive, shortens TI and TE through vagal and nonvagal pathways, increases tonic nonvagal and phasic vagal inputs, and stimulates more than one vagal fiber type.     

Bradyrhizobium japonicum mutants defective in root-nodule bacteroid development and nitrogen fixation

The genome of the slow-growing Bradyrhizobium japonicum (strain 110) was mutagenized with transposon Tn5. A total of 1623 kanamycin/streptomycin resistant derivatives were screened in soybean infection tests for nodulation (Nod) and symbiotic nitrogen fixation (Fix). In this report we describe 14 strains possessing a stable, reproducible Nod⁺Fix^- phenotype. These strains were also grown under microaerobic culture conditions to test them for free-living nitrogen fixation activity (Nif). In addition to strains having reduced Fix and Nif activities, there were also strains that had reduced symbiotic Fix activity but were Nif⁺ ex planta.Analysis of the genomic structure revealed that the majority of the strains had a single Tn5 insertion without any further apparent physical alteration. A few strains had additional insertions (by Tn5 or IS50), or a deletion, or had cointegrated part of the vector used for Tn5 mutagenesis. One of the insertions was found in a known nif gene (nifD) whereas all other mutations seem to affect different, hitherto unknown genes or operons.Several mutant strains had an altered nodulation phenotype, inducing numerous, small, widely distributed nodules. Light and electron microscopy revealed that most of these mutants were defective in different stages of bacteroid development and/or bacteroid persistence. The protein patterns of the mutants were inspected by two-dimensional gel electrophoresis after labelling microaerobic cultures with l-(³⁵S)methionine. Of particular interest were mutants lacking a group of proteins the synthesis of which was known to be under oxygen control. Such strains can be regarded as potential regulatory mutants.