Mutations in the bacteriophage lambda pL/oL region that spontaneously occur in plasmid pRPZ126

In a previous study (Chen and Porter, 1988), we isolated spontaneous mutations in a test plasmid that had occurred under non-selective conditions and assigned them to 1 of 6 different categories or groups. The test plasmid, pRPZ126, is a pBR322 derivative containing the bacteriophage lambda immunity region with the cI857 allele so that plasmid-containing cells shifted to 42 degrees C survive only if the expression of the lambda kil gene is prevented by mutation. 75% of the total spontaneous mutations obtained fall into two of these groups where there is no readily detectable change in plasmid size. The two groups differ in that the plasmids from the group 4 mutations are missing a specific HincII site while the plasmids from the group 5 mutations had no detectable plasmid change whatsoever. In this study, we randomly selected ten group 4 mutants and ten group 5 mutants and sequenced the lambda pL/oL region of the mutant plasmid. Of the ten group 4 mutants (HincII site missing), five involved a 24- or 44-basepair deletion in the pL/oL region of the plasmid. The other five group 4 mutants and four of the ten group 5 mutants were A-T to G-C transitions in the pL/oL region. The remaining six group 5 mutants did not demonstrate any sequence change in the pL/oL region of the plasmids. 8 out of 9 of these transition mutations occurred next to the 3' end of 3 different 5'-PyGGNPuNTG-3' sequences in the lambda operator region, and this same sequence is found adjacent to the A-T to G-C transition hotspot in the lac operator region (Schaaper et al., 1986). The 9th mutation, where the A-T to G-C transition occurred one basepair away from the lambda operator, was adjacent to a very similar sequence.

A computational procedure for assessing the significance of RNA secondary structure

In our recent series of papers, we have used the structures of statistical significance from Monte Carlo simulations to improve the predictions of secondary structure of RNA and to analyze the possible role of locally significant structures in the life cycle of human immunodeficiency virus. Because of intensive computational requirements for Monte Carlo simulation, it becomes impractical even using a supercomputer to assess the significance of a structure with a window size greater than 200 along an RNA sequence of 1000 bases or more. In this paper, we have developed a new procedure that drastically reduces the time needed to assess the significance of structures. In fact, the efficiency of this new method allows us to assess structures on the VAX as well as the CRAY.

The effect of intrauterine devices (stainless steel ring, copper-T220 and levonorgestrel) on the DNA content in isolated human endometrial cells

The effect of three different intrauterine devices on the DNA content in human endometrial cells has been studied in 29 women before and after the insertion of an IUD; a stainless steel ring (9 subjects), Copper-T220 (11 subjects) and a medicated IUD releasing levonorgestrel at a rate of 2 micrograms/day (9 subjects). The material was grouped into "bleeders" (having more than 8 days of bleeding and spotting per month) and "non-bleeders" (having less than 8 days of bleeding and spotting per month). The DNA content was assessed on isolated endometrial cells smeared from thin biopsies and the amount of DNA per cell nucleus was measured by means of a Feulgen microspectrophotometric method. No significant difference was found between the "bleeders" and the "non-bleeders" as to the DNA content. Nevertheless, when the total number of subjects were pooled together, a significant increase in the DNA content was found in the post-insertion specimens in the groups of women using the SS and the T-Cu IUDs. Furthermore, a significant decrease in the DNA content was also found when the specimens obtained after the insertion of the LNG IUD were compared with those obtained after 24 months' use of the stainless steel ring and the Copper-T220 device (p less than 0.01 and p less than 0.002, respectively). It is concluded that the insertion of an inert IUD or an T-Cu IUD, induces significant alterations in the DNA content of the human endometrium adjacent to the device, whereas the use of the LNG device does not significantly modify the DNA synthesis when used for 3-10 months. No correlation was found between the DNA content per cell and the number of days of bleeding and spotting.

The effect of intrauterine devices, the stainless steel ring, the copper T220, and releasing levonorgestrel, on the bleeding profile and the morphological structure of the human endometrium--a comparative study of three IUDs. A morphometric study of 96 cases

Thirty-four women using the stainless steel ring (SS), 43 women using the Copper T220 (TCu), and 19 women using levonorgestrel-releasing intrauterine devices (LNG) were admitted to the study. The light microscopic biopsy material was subjected to morphometric studies including 8 indices of endometrial activity before (Control) and after 24 months of exposure to the SS and TCu device and 3-10 months of exposure to the LNG device. The women were grouped into subjects with and without intermenstrual and prolonged bleeding. The results revealed that there were highly significant differences between the IUDs at the endometrial level as displayed by morphometry. However, the difference between bleeders and non-bleeders was not significant in any of the three types of IUDs. Although the mode of action of these IUDs at the endometrial level is different, the mechanism responsible for the irregular endometrial bleeding needs to be further investigated.

Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses

RNA stem-loop structures situated just 3' to the frameshift sites of the retroviral gag-pol or gag-pro and pro-pol regions may make important contributions to frame-shifting in retroviruses. In this study, the thermodynamic stability and statistical significance of such secondary structural features relative to others in the sequence have been assessed using a newly developed method that combines calculations of the lowest free energy of formation of RNA secondary structures and the Monte Carlo simulations. Our results show that stem-loop structures situated just 3' to the frameshift sites are both highly stable and statistically significant relative to others in the gag-pol or gag-pro and pro-pol junction domains (both 300 nucleotides upstream and downstream from the possible frameshift sites are included) of Rous sarcoma virus (RSV), human immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other more stable, or significant folding regions are predicted in these domains.

RNA secondary structures: comparison and determination of frequently recurring substructures by consensus

A method for assessing the preserved stem-loops of RNA secondary structures is presented. Frequently recurring helical stems in a set of secondary structures resulting from the simulated folding process of a given RNA are assessed and consensus structural motifs can then be selected to construct a secondary structure of the RNA. Alternatively, it can be applied to a series of 'optimal' and 'suboptimal' secondary structures computed using the dynamic program developed by Williams and Tinoco. To demonstrate the power and the usefulness of the program we give examples of this procedure.

Desmoplastic amelanotic melanoma of palate: a case report with immunohistochemistry and electron microscopic studies

A 24 year-old male with painful swelling over the right side of his palate for about two weeks was presented. An incisional biopsy was performed. In a routine hematoxylin and eosin examination by light microscopy, spindle and epithelioid cells with a bizarre appearance were discernible in the submucosal area. A pagetoid pattern was found in areas of the epithelium. Since this is not a remarkable finding, further examinations, such as the Trichrome-Masson and silver stain, immunohistochemistry using cytokeratin, vimentin, S-100, leukocyte common antigen, factor VIII, and alpha-1-antichymotrypsin detection kits, and electron microscopy were all carried out. According to the histological pattern of cells and the positive findings from the special stains, immunohistochemistry, and electron microscopy, a diagnosis of desmoplastic amelanotic melanoma was made. This variant of melanoma is a rare disorder with unremarkable, non-specific clinical manifestations in the oral cavity, which makes the diagnosis of this disease more difficult. We, therefore, report one case of this disease. Owing to the fact that diagnosis of this variant was mainly based on the positive findings of vimentin and S-100 in the immunohistochemistry examination and intracellular premelanosome detected by electron microscopy, immunodiagnosis and electron microscopy seem to be essential for differential diagnosis.

Gel electrophoretic analysis of DNA branched junctions

Gel electrophoresis has provided much of the detailed information we have about the properties of DNA junctions, stable branched molecules formed from oligonucleotide or polynucleotide strands. Here we review these applications, and present the results of an electrophoretic investigation of conformationally restricted junctions formed by covalently connecting two different pairs of strands in a junction with four arms. Native gel electrophoresis is employed to establish the formation and stoichiometry of the multistrand complexes. Ferguson analysis of native gel mobility shows that junctions have retardation coefficients that are distinct from those of linear DNA duplexes. Denaturing gel electrophoresis is the primary tool for characterizing junctions that have been covalently linked together to form both linear and macrocyclic oligomers of junctions (oligojunctions). Radioactively labelled strands enable one to monitor the progress of the ligation reaction: both linear and closed cyclic molecules result, and these can be distinguished by applying Ferguson analysis to denaturing gels. Combinations of exonuclease III, restriction enzymes and sequencing reactions have been applied to oligojunction molecules, and the results are all analyzed on denaturing gels. Junctions containing intramolecular "tethers" that restrict the conformation freedom of the complex comprise a new system for analyzing the conformations of branched molecules. In these tethered junctions, the ability of arms to move relative to each other is restricted substantially by covalently connecting pairs of arms in the original complex with short, flexible loops. The two tethers used here constrain the helical domains of the structure to be roughly parallel or anti-parallel. In this article, we use Ferguson analysis to compare two tethered junctions with an untethered junction. At high gel concentrations, the mobility of the untethered complex is found to be closer to that of the molecule tethered anti-parallel than to the one tethered parallel. Curvature in the Ferguson plots for all three of these junctions is detected over a range of compositions. At low gel concentrations, differences in electrophoretic mobility persist, suggesting that the untethered junction differs in charge as well as conformational freedom from the tethered analogs. We expect that studies of this kind will be able to define the conformational repertoire of junctions of different kinds, and to explore the effects of electrophoresis on these states.

Sequence divergence and open regions of RNA secondary structures in the envelope regions of the 17 human immunodeficiency virus isolates

Genetic variation during the course of infection of an individual is a remarkable feature of the acquired immune deficiency syndrome (AIDS) disease. This variation has been studied for the envelope protein encoding regions of seventeen different sequences from various isolates of human immunodeficiency virus (HIV) using multiple sequence comparison and calculation of variability. The open regions with little intramolecular base pairing in these envelope sequences are predicted by a recently developed statistical method. The minimum length L for a run of hypervariable sites, conserved sites, or open regions that gives significance at the 1% (or 0.1%) level is then determined by a scan statistical method. The results show that significant clusters of open regions predicted at the RNA levels correlate with significant clusters of hypervariable sites in the HIV envelope gene. Those significant genomic variations in HIVs seem to be manifested mainly in the extracellular portion of the envelope protein. Twelve potential antigenic determinants are predicted using an antigenic index method. Interestingly, the majority of the significant hypervariable regions in the exterior envelope protein (gp120) were predicted potential epitopes.

Automaticity of the SN and A-V junctional tissue before and after chemical denervation in the dog

Automaticity of SN and A-V junctional tissue was studied in 40 dogs in which a stable junctional rhythm was obtained following thermal ablation of the SN and sulcus terminalis. Atrial overdrive pacing studies were performed both before and after chemical denervation of the heart. Control sinus cycle and junctional CL were 438 +/- 13 ms and 751 +/- 23 ms, respectively. Chemical denervation resulted in significant prolongation of both junctional CL and maximal corrected junctional recovery time; junctional rate was down to 46 percent of the sinus rate observed before suppression of SN activity. Neither sinus CL nor maximal corrected SN recovery time changed significantly after administration of drugs. The basal autonomic nervous system has a relatively greater influence on the junctional pacemaker than on the normal SN in the dog and, when SN was suppressed, chemical denervation prolonged the junctional CL by 23 percent and junctional recovery time by 63 percent.

A cAMP-regulated chloride channel in lymphocytes that is affected in cystic fibrosis

A defect in regulation of a chloride channel appears to be the molecular basis for cystic fibrosis (CF), a common lethal genetic disease. It is shown here that a chloride channel with kinetic and regulatory properties similar to those described for secretory epithelial cells is present in both T and B lymphocyte cell lines. The regulation of the channels by adenosine 3',5'-monophosphate (cAMP)-dependent protein kinase in transformed B cells from CF patients is defective. Thus, lymphocytes may be an accessible source of CF tissue for study of this defect, for cloning of the chloride channel complex, and for diagnosis of the disease.

Common pitfalls in the evaluation of developmental screening tests

Wilson has written that screening puts a responsibility on the physician to provide some benefit to the person being screened. He made the distinction between the physician who is confronted by a patient with a problem that the physician may attempt to cure with unproved means, on one hand, and persons who mount community screening programs with unproved procedures on the other. He considers the former to be ethical and the latter unethical. Similarly, we consider the failure to avoid pitfalls--such as improper screening test administration, failure to use reliable outcome criteria, making inappropriate (although well-intentioned) predictions, and making inappropriate generalizations or drawing inappropriate conclusions--to be unethical. The pitfalls jeopardize the achievement of the desired outcome by screening programs. They also lead to inappropriate conclusions and possibly, therefore, to the use of inappropriate tests. If the scientific community does not take steps to avoid such pitfalls in developmental screening, it invites those who make health care decisions to eliminate such screening or to mandate procedures which may not be scientifically sound. Neither of these alternatives is acceptable. The only alternative, first, is to ensure that one avoids common pitfalls when screening in one's own practice and, second, to be on guard against developmental screening studies and reports that fail to avoid these errors.

Construction and analysis of monomobile DNA junctions

Immobile DNA junctions are complexes of oligomeric DNA strands that interact to yield branched structures in which the branch point cannot migrate. This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed "monomobile", contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.

An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors

Current secondary structure prediction computations have a serious drawback. The calculated thermodynamically most stable structure often differs from that observed in solution or in crystal form. In this paper we suggest a way to partially over-come some of these limitations by simulating the RNA folding process and calculating the frequencies of occurrence of the various substructures obtained. The frequently recurring substructures are then selected to construct the secondary structure of the whole RNA. 142 tRNA molecules and an E. coli 16S rRNA molecule have been examined by this method. The percentage of successful prediction of the correct helices are significantly higher than those calculated previously. The secondary structures of intervening sequences (IVSs) excised from human alpha-like globin pre-mRNAs are also computed. Thus, in this method the secondary structures obtained are composed of the statistically more significant substructures. This has also been demonstrated by using randomly shuffled sequences. The secondary structures of each of the randomized sequences are computed and their mean and standard deviations are used in evaluating the significance of the substructures obtained in the folding of the biological sequence. Some potentially appealing structural features aligning adjacent exons for ligation have been found.

Tracts of A.T base pairs retard the electrophoretic mobility of short DNA duplexes

An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A.T base pairs causes a duplex to move more slowly than does any combination of isolated A.T pairs This behavior appears to be an intrinsic property of these sequences, since the anomaly persists in the absence of magnesium or presence of spermine and is not due to strand dissociation. In two decamers we studied, the position of A.T tracts within a duplex can be shown to influence mobility: the sequence GA4T4C associated with bending or curvature of the helix axis when ligated into polymers migrates more slowly than the corresponding sequence GT4A4C, polymers of which migrate as linear B DNA.

Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-I)

The stability of potential RNA stem-loop structures in human immunodeficiency virus isolates, HTLV-III and ARV, has been calculated, and the relevance to the local significant secondary structures in the sequence has been tested statistically using a Monte Carlo simulation method. Potentially significant structures exist in the 5'non-coding region, the boundary regions between the protein coding frames, and the 3' non-coding region. The locally optimal secondary structure occurring in the 5' terminal region has been assessed using different overlapping segment sizes and the Monte Carlo method. The results show that the most favorable structure for the 5' mRNA leader sequence of HIV has two stem-loops folded at nucleotides 5-104 in the R region (stem-loop I, 5-54 and stem-loop II, 58-104). A large fluctuation of segment score of the local optimal secondary structure also occurs in the boundary between the exterior glycosylated protein or outer membrane protein and transmembrane protein coding region. This finding is surprising since no RNA signals or RNA processing are expected to occur at this site. In addition, regions of the genome predicted to have significantly more open structure at the RNA level correlate closely with hypervariable sites found in these viral genomes. The possible importance of local secondary structure to the biological function of the human immunodeficiency virus genome is discussed.

Reappraisal of atrioventricular junctional pacemaker automaticity in the sick sinus syndrome. Clinical significance and the role of autonomic chronotropic influences

Postpacing impulse recovery times of the junctional tissue (junctional automaticity) were determined by atrial or ventricular overdrive pacing in 27 patients with dysfunction of the sinus node. The maximum junctional recovery time (MJRT) could be measured in 22 patients and ranged from 1,630 to 9,730 ms (mean 3,860 +/- 2,077); the maximum corrected junctional recovery time (MJRTc) could be measured in 18 patients and ranged from 140 to 5,986 ms (mean 2,089 +/- 1,529). Autonomic influence on the JRTs was evaluated by intravenous administration of atropine (1.5 mg) alone or in combination with propranolol (5 to 6 mg). Of the seven patients in whom MJRTc and/or MJRT could be measured before and after drug intervention, the JRTs shortened in four and prolonged in three after combination of atropine and propranolol. Atropine alone shortened MJRT in all eight patients studied. Our data reveal that both vagal and catecholamine-dependent factors (especially vagal over-activity) are operative in the escape mechanism of the junctional tissue.

Complementary DNA clones of chicken proto-oncogene c-ets: sequence divergence from the viral oncogene v-ets

The avian acute leukemia virus E26 induces erythroblastosis and myeloblastosis in chickens. The oncogene of this virus includes sequences derived from the cellular gene designated c-ets, which is normally expressed in lymphoid cells and whose product is a protein of apparent molecular weight ca. 54,000 daltons. Complementary DNA clones representing the major transcript of the chicken c-ets proto-oncogene were isolated from a spleen cell library. Sequence analysis of the cDNA revealed that it contains an open reading frame encoding a polypeptide of 441 amino acids with a molecular weight of 49,932 daltons. This open reading frame can be transcribed and translated in vitro into a 50 kd protein that is specifically immunoprecipitated with antiserum to the v-ets oncogene product. Within the central region of homology between c-ets and v-ets, there are only 5 nucleotide substitutions resulting in 4 amino acid changes. However, coding sequences at the 5' and 3' ends of the v-ets oncogene and the chicken c-ets cDNA differ from one another. These changes may be responsible for the differential functions of c-ets and v-ets in cells of different hematopoietic lineages and may account for the pathogenic properties of the v-ets oncogene.