An improved DNA sequencing strategy

A modification of Hong's systematic DNA sequencing strategy is described. The original procedure has been simplified and transfectant yield increased. After DNase I limited cleavage in the presence of Mn2+, the single-cut linear DNA does not have to be separated from supercoiled or open circular DNA on an agarose gel. After ligation, the DNA is digested with a second restriction endonuclease for which a unique cleavage site resides between the insert and the first restriction endonuclease cutting site. The original intact DNA is linearized whereas the deleted subclone is not. The background is decreased to an undetectable level. This DNA sequencing strategy was tested on a 1.4-kb DNA fragment containing the araC regulatory gene from Erwinia carotovora. A set of subclones sufficient to sequence the fragment on both strands was produced in 2 days and the yield was at least 60-fold higher than in the original protocol.

The araBAD operon of Salmonella typhimurium LT2. I. Nucleotide sequence of araB and primary structure of its product, ribulokinase

Hybrid plasmids containing the araBAD operon of Salmonella typhimurium LT2 were characterized by Southern blot and genetic analyses. The nucleotide sequence of araB was determined. The araB gene product, ribulokinase (EC 2.7.1.16), was purified and the results of amino acid composition analysis and partial amino acid sequence are in agreement with predictions from the DNA sequence. Ribulokinase is 569 amino acid residues long and has a calculated Mr of 61 793. Ribulokinase shares significant homology with xylulose kinase from Escherichia coli. Codon usage in the araB gene does not favor those codons which have intermediate codon-anticodon binding energy.

The araBAD operon of Salmonella typhimurium LT2. III. Nucleotide sequence of araD and its flanking regions, and primary structure of its product, L-ribulose-5-phosphate 4-epimerase

The araD gene of Salmonella typhimurium LT2 consists of 744 nucleotides and has an ORF coding for a protein of 248 amino acid residues with a calculated Mr of 27059. The product of araD, L-ribulose-5-phosphate 4-epimerase, was purified and the amino terminal sequence was determined. It is identical to that predicted by the ORF. A 143-bp intercistronic region was found between the araA and araD genes which can form stem-loop structures with calculated free energies of up to -76.7 kcal/mol. Three sets of sequences within this 143-bp region are comparable to a consensus sequence deduced from several known intercistronic regions. Approximately equimolar amounts of the araBAD operon products were present in L-arabinose-induced cells. Sequences similar to both rho-independent and rho-dependent transcription terminators are present after the araD gene.

Cloning of the pectate lyase genes from Erwinia carotovora and their expression in Escherichia coli

A hybrid cosmid coding for pectate lyase (PL) activity was identified from an Erwinia carotovora genomic library by an immunological screening method. A 7-kb DNA fragment was identified which codes for three proteins identical in size to proteins with PL activity purified from E. carotovora culture supernatants. The three proteins had apparent Mrs of 41, 44 and 44 X 10(3) as estimated by SDS-PAGE. None of the PLs were exported from Escherichia coli strain HB101 but all were found in the periplasmic space. Plant tissue was macerated by the PLs made in E. coli.

The araBAD operon of Salmonella typhimurium LT2. II. Nucleotide sequence of araA and primary structure of its product, L-arabinose isomerase

The nucleotide sequence of gene araA of Salmonella typhimurium LT2 has been determined. The gene encodes an L-arabinose isomerase (EC 5.3.1.4) of 500 amino acid residues with a calculated Mr of 55814. The ATG start codon of araA is 10 bp distal to the TAA termination codon of araB. A presumed ribosome-binding site (RBS) "TAAGGA" 7 bp from the ATG codon overlaps the stop codon of araB. L-Arabinose isomerase was purified and the amino acid composition is in agreement with that predicted from the DNA sequence. The NH2-terminus of the protein is modified as the sequence cannot be analyzed by the automated Edman degradation. Amino acid composition analyses of both NH2-terminal and C-terminal cyanogen bromide (CNBr) cleaved peptides and partial amino acid sequence of the C-terminal peptide are consistent with the deduced amino acid sequence.

Structure and composition of microcalcifications in benign and malignant lesions of the breast: study by light microscopy, transmission and scanning electron microscopy, microprobe analysis, and X-ray diffraction

Microcalcifications previously located by radiography were extracted from 25 fresh specimens obtained from patients who had undergone tumorectomy or systematized mammary exeresis. Two principal types of microcalcifications were distinguished: Type I microcalcifications were amber in color and generally crystalline on scanning electron microscopy, with only one calcium peak on microprobe analysis; x-ray diffraction revealed that weddellite was involved. Type II microcalcifications were whitish, nonbirefringent under polarized light, and generally ovoid or fusiform, with two peaks, one calcium and the other phosphorus, on microprobe analysis; these microcalcifications were composed of calcium phosphate, the most characteristic form of which is hydroxyapatite, in the form of needles arranged in rosettes on transmission electron microscopy. Type I microcalcifications were observed in four of eight benign breast lesions, in two of three in situ lobular carcinomas, and in no intraductal adenocarcinomas or infiltrating carcinomas. Type II microcalcifications were present in all infiltrating carcinomas and intraductal adenocarcinomas; they were also found in benign lesions (four of eight) and even associated with type I microcalcifications in one in situ lobular carcinoma. There are, therefore, no "benign" or "malignant" microcalcifications; however, the presence of weddellite is a strong indication that a lesion is benign or, at most, an in situ lobular carcinoma.

High tension electrical burns of upper arms treated by segmental excision of necrosed humerus. An introduction of a new surgical method

This paper describes treating high-tension electrical burns of the upper arms by segmental excision of the necrosed humerus. This is a new surgical method of treating local electrical burns. The authors use modification of traditional surgical method, shorten the course of treatment, and preserve the injured limb. However, this surgical method should not be used to treat all high-tension electrical burns of the upper arm, and should be used only under certain conditions. Therefore, it is important to grasp the operative indications.

The nucleotide sequence of the araC regulatory gene in Salmonella typhimurium LT2

The nucleotide sequence of the araC regulatory gene of Salmonella typhimurium LT2 has been determined. This sequence and the predicted araC translational product are compared to their counterparts in Escherichia coli. The two genes code for similar products although the S. typhimurium protein is eleven amino acids shorter than the E. coli protein. The predicted amino acid sequences are 92% conserved and the DNA sequences are 82% conserved for the common regions of the two genes.

Surface activities of tertiary amine local anesthetics at air/water interface in the presence and absence of phospholipid monolayers

Adsorption of procaine and tetracaine to the dipalmitoyl phosphatidylcholine monolayers at the air/water interface is analyzed in terms of two types of interaction: (1) between the phospholipid molecules and the ligand molecules, and (2) among the ligand molecules themselves. The presence of the phospholipid monolayer increases the surface concentration of the anesthetics. The interaction energy, omega AB, between the phospholipid molecules and the anesthetic molecules at the interface accounts for this excess adsorption. The values were --2.95 kT for procaine and --2.99 kT for tetracaine where k is the Boltzmann constant and T = 298 K. The adsorption of the local anesthetics to the interface was cooperative. The interaction energy, omega AA, between the anesthetics molecules on the surface determines the cooperativity. The values were --0.056 kT for procaine and --0.397 kT for tetracaine, where T = 298 K. This parameter determines the slope of the curve plotted relating the surface concentration (gamma) and the logarithm of the bulk concentration (log C). When (omega AA/kT) greater than or equal to 1, the adsorption follows the phase-transition. A parameter KA, which is related to the difference of the free energy of anesthetics between the surface and the bulk molecules, locates the take-off point of the adsorption curve at the log C axis. The values were 2.15 x 10(3) for procaine and 7.00 x 10(3) for tetracaine. In spite of the general assumption that the difference in the clinical potency among local anesthetics are attributable to their lipid solubility, the present results showed that the phospholipid-anesthetic interaction energies for procaine and tetracaine were similar. The larger surface concentration of tetracaine than procaine at the same bulk concentration was due to the combined effect of KA and omega AA. KA represents the tendency of the anesthetic molecules to escape from the hydrogen-bonded water phase, and omega AA determines the cooperativity factor causing these molecules to aggregate at the interface. It was also observed that the charged forms of the anesthetics have non-zero surface activities.

Variation of isomer distribution in electrophilic nitration of toluene, anisole, and o-xylene: Independence of high regioselectivity from reactivity of reagent

The nitration of toluene and anisole was studied with nitrating systems of varying reactivity. High regioselectivity of ortho-para over meta substitution was maintained in all nitrations, regardless of the reactivity of the nitrating system. At the same time, the amount of meta substitution stayed low (3% or less), even when the fast reactions may have reached the encounter-controlled limit. Because the nitration of o-xylene, in which both ring positions are activated by the effect of a methyl group, also does not show any diminishing of regioselectivity, the possibility of a dual mechanistic pathway, in which the activated position would react by a fast, encounter-controlled path, whereas the nonactivated meta position by a slower sigma-type path, can be ruled out. The data unambiguously prove that the high regioselectivity of electrophilic aromatic nitration is independent of the reactivity of the reagent, because no significant increase of meta substitution of toluene or anisole was observed, regardless of the activity of the nitrating system. No selectivity-reactivity relationship is thus evident and the ortho-para directing effect of primary substituents over meta substitution is always maintained. The variation in the amount of the meta isomer, up to the observed limit of about 3% in the case of toluene and <2% for anisole, is probably significant but, at the present time, cannot be quantitatively evaluated with the +/-0.5% overall reproducible accuracy of the nitrations. Steric factors, such as increasing bulkiness of the nitrating agent, also can affect the ortho-para isomer ratios but are not considered to be the only reason for the observed variations, which reflect the specific nitrating systems, affecting the nature and position of the transition state of highest energy on the reaction pathway.

Multiple factor analysis of the action of local anesthetics

The pH jump data of Bianchi and Strobel [(1968) Trans. N.Y. Acad. Sci. Ser. II, 30, 1082-1092] on desheathed frog sciatic nerve are fitted to rate equations. A general quantitation of synergism, summation, and antagonism of anesthetics and of excitation is given.