A program for predicting significant RNA secondary structures

We describe a program for the analysis of RNA secondary structure. There are two new features in this program. (i) To get vector speeds on a vector pipeline machine (such as Cray X-MP/24) we have vectorized the secondary structure dynamic algorithm. (ii) The statistical significance of a locally 'optimal' secondary structure is assessed by a Monte Carlo method. The results can be depicted graphically including profiles of the stability of local secondary structures and the distribution of the potentially significant secondary structures in the RNA molecules. Interesting regions where both the potentially significant secondary structures and 'open' structures (single-stranded coils) occur can be identified by the plots mentioned above. Furthermore, the speed of the vectorized code allows repeated Monte Carlo simulations with different overlapping window sizes. Thus, the optimal size of the significant secondary structure occurring in the interesting region can be assessed by repeating the Monte Carlo simulation. The power of the program is demonstrated in the analysis of local secondary structures of human T-cell lymphotrophic virus type III (HIV).

Effect of diapause hormone on cyclic nucleotide metabolism in developing ovaries of the silkworm, Bombyx mori

1. The content of cyclic AMP and cyclic GMP in ovaries of the silkworm, Bombyx mori, changed differently depending on development. 2. The extirpation of suboesophageal ganglion caused cyclic AMP to decrease and cyclic GMP to increase at different developmental stages. 3. The reversed changes in the cyclic nucleotides were brought about by implantation of the ganglion or by injection of the diapause hormone preparation. 4. No change in both cyclic nucleotides was induced in ovaries during the first 24 hr after an injection of the hormone, but the clear effects appeared after a lag phase of a few days.

Characterization of the types of mutational events that spontaneously occur in a plasmid system

The immunity region from a cI857 derivative of bacteriophage lambda has been cloned into the EcoRI site of pBR322 to produce a plasmid that can be used to analyze spontaneous mutagenesis. Cells containing this plasmid are temperature-sensitive for growth unless mutations have occurred that somehow prevent the expression of the kil gene in the lambda fragment at non-permissive temperature. 678 such temperature-resistant mutants from 10 independent subcultures each of 2 different recA- E. coli strains have been collected, and the nature of the plasmid mutations obtained has been analyzed. All of the subcultures contained mutants that allowed growth at the restrictive temperature without showing a detectable change in plasmid size. 75% of the total mutants fell in this class. More than half of these mutations involved the lambda leftward promoter, pL, and such mutants were found in all 20 subcultures. The remaining 25% of the mutations involved a change in plasmid size and mutations of this class were found in 18 of 20 subcultures. 12% of the total mutants (found in 16 of 20 subcultures) had an insertion of IS1 in the region between pL and the lambda kil gene. 6% of the total mutants had undergone an IS1-mediated deletion, while 1% were mixed colonies in which multiple IS1-mediated events had occurred. About 1% of the total mutants had undergone complex IS1-mediated DNA rearrangement(s) that have not yet been characterized. In total, 11 of 20 subcultures yielded isolates where IS1-mediated rearrangements had occurred. The remaining 4% of the mutations included insertions of IS5, IS30, and an IS1 family member that appears to be IS1T as well as IS1T-mediated deletions and deletions that do not appear to have been mediated by any insertion sequence. A mutant with both an IS1 insertion and an alteration involving pL has also been isolated.

There are two C4 genetic loci and a null allele in the chimpanzee

Genetic polymorphism in C4 in the chimpanzee was studied by agarose gel electrophoresis of desialated plasma and development of patterns by immunofixation with antiserum to human C4 and by a C4-sensitive hemolytic overlay. In general, immunofixation patterns showed multiple partially overlapping bands of which only the most cathodal had strong hemolytic activity. In analogy to human C4, the latter were designated C4B, whereas those detected by immunofixation which had little hemolytic activity were designated C4A. Chimp C4A and C4B reacted with human and mouse (monoclonal) anti-C4B and human anti-Ch1 but neither reacted with monoclonal anti-C4A or human anti-Ch2, Ch3, Rg1, or Rg2. On sodium dodecyl sulfate polyacrylamide gel electrophoresis, the alpha chain of C4B showed a slightly lower apparent relative mass than that of C4A at around Mr 93,000. There were three C4A variants and two C4B variants inherited in families as autosomal codominant traits, as C4A-C4B cosegregating pairs with no detectable crossing-over. These pairs were inherited with chimpanzee leukocyte antigen types C2 and BF variants without detectable crossing-over. Half-null C4 haplotypes with C4B QO were observed in family studies. Nine BF, C2, C4A, C4B allelic haplotypic combinations (complotypes) were identified among presumably unrelated chimpanzees.

A Yersinia pseudotuberculosis protein which cross-reacts with HLA-B27

The most-debated question in the investigation of the spondyloarthropathies has been whether there is molecular mimicry between host HLA-B27 antigens and the arthritis-causing pathogens. We have generated a monoclonal anti-HLA-B27 antibody in our laboratory and have used a radioimmunoassay to screen a panel of bacterial species. Two strains of Yersinia pseudotuberculosis were found to be highly reactive. The cross-reactive Yersinia component was identified by Western blot to be a 19,000 component. A preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis chromatography apparatus was constructed to isolate milligram quantities of this component. To verify that the component carried the HLA-B27-specific epitope, rabbits were hyperimmunized with the purified materials. Affinity-purified antibodies from one of the immunized rabbits indeed carried anti-HLA-B27 activity. Last, antibodies generated against synthetic peptides derived from the HLA-B27.1 amino acid sequence were tested against the Yersinia component. Positive reactivity was found with antibodies generated against a peptide spanning residues 69-83 of the HLA-B27.1 protein. Since this resides in the segment responsible for the allotypic specificity of the antigen, these experiments establish the presence of molecular mimicry to a high degree of confidence.

A Yersinia pseudotuberculosis protein which cross-reacts with HLA-B27

The most-debated question in the investigation of the spondyloarthropathies has been whether there is molecular mimicry between host HLA-B27 antigens and the arthritis-causing pathogens. We have generated a monoclonal anti-HLA-B27 antibody in our laboratory and have used a radioimmunoassay to screen a panel of bacterial species. Two strains of Yersinia pseudotuberculosis were found to be highly reactive. The cross-reactive Yersinia component was identified by Western blot to be a 19,000 component. A preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis chromatography apparatus was constructed to isolate milligram quantities of this component. To verify that the component carried the HLA-B27-specific epitope, rabbits were hyperimmunized with the purified materials. Affinity-purified antibodies from one of the immunized rabbits indeed carried anti-HLA-B27 activity. Last, antibodies generated against synthetic peptides derived from the HLA-B27.1 amino acid sequence were tested against the Yersinia component. Positive reactivity was found with antibodies generated against a peptide spanning residues 69-83 of the HLA-B27.1 protein. Since this resides in the segment responsible for the allotypic specificity of the antigen, these experiments establish the presence of molecular mimicry to a high degree of confidence.

Precise Timing of the Last Interglacial Period from Mass Spectrometric Determination of Thorium-230 in Corals

The development of mass spectrometric techniques for determination of (230)Th abundance has made it possible to reduce analytical errors in (238)U-(234)U-(230)Th dating of corals even with very small samples. Samples of 6 x 10(8) atoms of (230)Th can be measured to an accuracy of +/-3 percent (2sigma) and 3 x 10(10) atoms of (230)Th can be measured to an accuracy of +/-0.2 percent. The time range over which useful age data on corals can be obtained now ranges from about 50 to about 500,000 years. For young corals, this approach may be preferable to (14)C dating. The precision with which the age of a coral can now be determined should make it possible to critically test the Milankovitch hypothesis concerning Pleistocene climate fluctuations. Analyses of a number of corals that grew during the last interglacial period yield ages of 122,000 to 130,000 years. The ages coincide with, or slightly postdate, the summer solar insolation high at 65 degrees N latitude which occurred 128,000 years ago. This supports the idea that changes in Pleistocene climate can be the result of variations in the distribution of solar insolation caused by changes in the geometry of the earth's orbit and rotation axis.

Systemic lupus erythematosus in children

A retrospective study was made of 137 children with systemic lupus erythematosus (SLE) seen at the Veterans General Hospital in the past 12 years. There were 116 females (84.7%), and 21 males (15.3%). The peak ages of onset were 13-14 years and 16-17 years. Malar rash, arthritis and fever were the most common presentations, as in previous studies. Central nervous system (CNS) involvement occurred in 24 cases (17.5%), and renal disorder was noted in 77 cases (56.2%). Renal biopsy in 67 cases showed a pathological transformation rate of 16.1% (5/31). Ten patients died during the study period, with renal insufficiency the primary cause of death.

Controlled trial of acupuncture for disabling breathlessness

In a randomised controlled trial, twelve matched pairs of patients with chronic obstructive pulmonary disease received traditional Chinese acupuncture or placebo acupuncture. After three weeks' treatment the traditional-acupuncture group showed significantly greater benefit in terms of subjective scores of breathlessness and six-minute walking distance. Objective measures of lung function were unchanged in either group. Whether these differences are mediated by endogenous opiate and/or peptide release remains speculative.

Terminal cardiac electrical activity in adults who die without apparent cardiac disease

Prolonged electrocardiographic (Holter) recording was performed to analyze terminal electrical events in 23 hospitalized adults who died without apparent cardiac disease. Most patients showed a gradual slowing of heart rate with shifting of cardiac pacemaker downward from the sinus node or atria to the atrioventricular junction and ventricles, resulting in cardiac asystole. Dominant bradyarrhythmia was more common than ventricular tachyarrhythmia (83 vs 17%). Agonal ST-segment elevation was not uncommon (26%). These terminal electrical events became manifest from 1 to 450 minutes (mean 62) before cessation of cardiac electrical activity. Forty-eight percent of the patients continued to show deteriorating sinus or atrial activity up to the last moment. The mechanism of bradycardiac asystole in patients with no apparent cardiac disease may be attributed to generalized anoxic and toxic depression of the sinus node and subsidiary pacemakers, together with neurogenic suppression of these structures.

Antibodies to distal carboxyl terminal epitopes in the v-fms-coded glycoprotein do not cross-react with the c-fms gene product

The product of the v-fms oncogene is an integral transmembrane glycoprotein that is closely related to the cell surface receptor for the macrophage colony stimulating factor, CSF-1. A fragment of the v-fms gene encoding a major portion of the extracellular amino terminal domain, the membrane-spanning segment, and the entire carboxyl terminal tyrosine kinase domain of the glycoprotein was molecularly cloned into an inducible prokaryotic expression plasmid. Polypeptide products consisting only of v-fms-coded amino acids were produced in bacteria and were used to prepare immune reagents that precipitated the v-fms-coded glycoproteins expressed in transformed cells. Whereas rabbit antisera to recombinant polypeptides detected antigenic determinants of the c-fms proto-oncogene product, seven mouse monoclonal antibodies to these same antigens reacted only with v-fms-specific epitopes. Proteolytic mapping experiments and studies with a mutant v-fms-coded glycoprotein lacking the 37 carboxyl terminal amino acids of the wild-type product showed that the monoclonal antibodies were restricted in their reactivity to epitopes at the extreme carboxyl terminus of the glycoprotein. The v-fms and c-fms gene products must differ significantly in this region.

[Epidemiologic investigation of carcinoma of the esophagus and gastric cardia carcinoma in Nanao County, Guangdong province]

Nanao county, Guangdong province is a high incidence area of carcinoma of esophagus and gastric cardia carcinoma. By retrospective investigation of data in the past 14 years (1970 to 1983), the annual average crude mortality of carcinoma of esophagus and gastric cardia carcinoma was found to be 88.65/100,000, the age adjusted mortality of Chinese population was 82.91/100,000 and that of the world population was 113.09/100,000. The mortality of the male was 100.65/100,000 and of the female was 67.24/100,000 with the ratio of 1.38:1. As regards the relationship between the age and mortality, the highest rate occurs from 50 to 74. A higher mortality was also observed in the population engaged in salt production and fishing. The mortality was higher in the lower elevation areas than in the elevated regions.

Frequency of various congenital heart diseases in Chinese adults: analysis of 926 consecutive patients over 13 years of age

A retrospective analysis was performed in 926 consecutive Chinese persons, aged 14 to 68 years, in whom congenital heart disease had been diagnosed and catheterization had been performed over the past 24 years. The incidence of various congenital cardiac malformations was compared with that in other series reported world-wide. About 60% of the 926 patients underwent surgery, and anatomic details of the malformations were examined. Congenital aortic valvular stenosis and coarctation of the aorta were uncommon (2.4% and 1.2%, respectively) among the Chinese adults, and the ethnic differences with Western countries in the incidence of these 2 defects were apparent and real. In contrast, aneurysm of the sinus of Valsalva, either ruptured or nonruptured, was more common (4.3%) and the incidence of outlet muscular type (or type 1) of ventricular septal defect was 4 to 9 times as common as has been reported in the West. Genetic differences rather than environmental factors or dietary habits may explain these special features.

The proto-oncogene c-ets is preferentially expressed in lymphoid cells

The transforming sequences of the avian acute leukemia virus, E26, contain two distinct oncogenes, v-mybE and v-ets, fused together. By using a probe containing v-ets sequences, polyadenylated transcripts of the c-ets proto-oncogene were detected in avian tissues; they included a major 7.0-kilobase and a minor 2.0-kilobase species. These c-ets mRNAs were detected at high levels only in lymphoid organs and in avian T and B lymphoid cell lines. A similar pattern of c-ets transcription was observed in human hematopoietic cell lines, with transcripts detected in lymphoid B and T cells but not in erythroid or myeloid cells. The E26 oncogene was inserted into an inducible expression vector, and a 90-kilodalton protein (bp90) was produced in bacteria. Rabbit antisera raised to purified bp90 precipitated P135gag-mybE-ets, the v-mybE-ets polyprotein expressed in E26-transformed cells, and also reacted with p50v-mybA, the transforming protein of the avian myeloblastosis virus. Antiserum to bp90 was absorbed with a bacterially synthesized v-mybA protein to remove anti-myb activity. The absorbed anti-bp90 serum retained the ability to immunoprecipitate P135gag-mybE-ets from E26-transformed cells and specifically reacted with a 56-kilodalton polypeptide (p56) detected in chicken lymphoid organs and in T and B lymphocytes of both avian and human origin. The data suggest that p56 is a translational product of the c-ets proto-oncogene and imply that p56 may be involved in regulating the growth of lymphoid cells.