Secondary structure of 7SK and 7-2 small RNAs. Possible origin of some 7SK pseudogenes from cDNA formed through self-priming by 7SK RNA

Pseudogenes having homology to small RNAs, like 7SL, 7SK, 6S, 4.5S, U1, U2, and U3 RNAs, are abundant and dispersed in the genomes of higher eukaryotes [reviewed in Weiner et al. (1986) Annu. Rev. Biochem. 55, 631-661]. To understand better the possible origin of these pseudogenes, we studied the abilities of cytoplasmic 7SL, 7SK, and nucleolar 7-2 RNAs to self-prime and result in the synthesis of cDNAs. When rat 7SK RNA was used as substrate, a 294-nucleotide-long cDNA was synthesized in vitro by reverse transcriptase, indicating that the 3' end of 7SK RNA can act in a self-priming manner to generate 7SK cDNA. When 7-2 RNA was used as a substrate, a cDNA of approximately 235 nucleotides was observed; 7SL RNA did not act as a self-primer. Earlier studies have shown that DNAs homologous to 7SK RNA are represented by a moderately reiterated family in the mammalian genomes and many of these sequences were found to be truncated 7SK pseudogenes [Murphy et al. (1984) J. Mol. Biol. 177, 575-590]. In this study, one 7SK clone from the rat genome was characterized by sequencing. This clone contained 243 base pairs homologous to the 5' end of 7SK RNA, and was flanked by direct repeats. These data suggest that, as previously proposed for some U3 pseudogenes [Bernstein et al. (1983) Cell 32, 461-472], one mechanism for the generation of truncated 7SK pseudogenes may be the integration of self-primed reverse transcripts of 7SK RNA at random genomic sites.

Students performance vs. hospital performance in the labor market for medical interns and residents. Do hospitals perform better due to asymmetry in information available to them relative to students?

This paper concerns the labor market for medical interns and residents in the U.S., and in particular, the question of whether the current matching mechanism between graduating medical students and hospitals is 'informationally inefficient'. It was found that overall students performed better than hospital programs in contrast to the common claim that hospitals are more likely to perform better due to seeming superiority in analyzing publicly available information or through access to non-publicly available information. We also conducted a similar analysis for the different specialty programs. In six specialty programs the students' performance was better than hospitals, in two specialty programs the hospitals performance was better than the students and in 14 specialty programs the difference in performance was not statistically different from zero. Thus, only in two cases the hypothesis that the specialty market is informationally inefficient cannot be rejected using the data available. It should be noted that this market is atypical (compared with other labor markets) in that we can test whether it is informationally inefficient by using a practical definition adopted from the field of finance.

Rat nucleolar 7-2 RNA is homologous to mouse mitochondrial RNase mitochondrial RNA-processing RNA

7-2 RNA (also termed RNA M and 7SM RNA) is a noncapped small RNA present in small ribonucleoprotein particles; these particles are present in the granular compartment of the nucleolus. Some sera from patients with scleroderma specifically immunoprecipitate 7-2 RNA-containing particles (Hashimoto, C., and Steitz, J. A. (1983) J. Biol. Chem. 258, 1379-1382; Reddy, R., Tan, E. M., Henning, D., Nohga, K., and Busch, H. (1983) J. Biol. Chem. 258, 1383-1386; Reimer, G., Raska, I., Scheer, U., and Tan, E.M. (1988) Exp. Cell Res. 176, 117-128). In this study, the primary sequence of Novikoff hepatoma 7-2 RNA was determined and a possible secondary structure is presented. The Novikoff hepatoma 7-2 RNA is 94% homologous to the recently described mouse mitochondrial RNase MRP RNA, suggesting that Novikoff hepatoma 7-2 RNA may be the homologue of mouse MRP RNA. The presence of 7-2 RNA in nucleoli and in mitochondria suggests that 7-2 ribonucleoproteins, in addition to being essential components of mitochondrial RNase, may also be functional in nucleolar RNA processing and ribosome biogenesis.

Genes for human U3 small nucleolar RNA contain highly conserved flanking sequences

Six human genomic clones containing sequences homologous to the U3 small nuclear RNA (snRNA) were isolated and characterized. Four of these clones were real U3 snRNA genes because they were transcribed in frog oocytes and the DNA sequences corresponding to the U3 snRNA were identical to the U3 snRNA of HeLa cells. The nucleotide sequences of four true U3 snRNA genes, 537 nucleotides on the 5'-flanking region and 340 nucleotides on the 3'-flanking region, were found to be identical. In addition, the restriction patterns, upto 2 kb on the 5' side and 2.2 kb on the 3' side, appeared to be same. All the isolated U3 clones, containing 15-20 kb of genomic DNA, contained only one U3 snRNA gene, indicating that the human U3 snRNA genes are several kilobases apart. One of the U3 clones contained a full-length U3 pseudogene. Southern blot analysis of genomic DNA with cloned U3 DNA as probe indicated that human DNA contains two families of U3 genes which differ in their flanking sequences. In the 5' flanking region of human U3 snRNA genes, homology to U-gene promoter element, an octamer motif, the 'U3 box', SP1 binding sites and a consensus 3' box in the 3' flanking region, were observed. These data show that the genomic organization and the sequence motifs that control transcription of human nucleolar U3 snRNA genes are similar to those of human U1 and U2 snRNA genes and suggest common mechanism(s) in the evolution of snRNA genes.

Does the intraesophageal pH probe accurately detect acid reflux? Simultaneous recording with two pH probes in humans

Little is known about the accuracy of intraesophageal pH monitoring, ie, do false negatives occur? This study was designed based on the assumption that if two pH probes are placed equidistant from a distal acid source, and the probes measure different values, then one probe might miss acid if it were there alone. We performed 24-hr intraesophageal pH monitoring in 10 patients with gastroesophageal reflux disease, simultaneously placing two pediatric pH probes (probes A and B) 5 cm proximal to the LES in such close proximity that one would expect only small differences in the acid exposure measured by the probes. However, the amount of acid exposure measured by probes A and B differed greatly in some instances. Individual probe performance does not alone account for these differences, since, when pH recordings were reviewed, one probe was as likely to miss acid exposure as the other. These differences would result in a change in the clinical diagnosis in two of 10 patients. Variability in the number of episodes was great and occurred even when there was concordance in percent acid exposure. These data raise questions about the absolute accuracy of the pH probe as the gold standard in the measurement of gastroesophageal reflux.

Nucleotide and deduced amino acid sequences for the four variable domains of the major outer membrane proteins of the 15 Chlamydia trachomatis serovars

The amino acid sequences of major outer membrane proteins (MOMPs) from Chlamydia trachomatis serovars A, B, C, L1, and L2 are predominantly conserved but have four variable domains (VDs) in which major neutralizing and serotyping antigenic determinants are located. Because these MOMP VDs are primarily responsible for antigenic differences between serovars and are associated with important immunological and biological properties, we undertook studies focused on defining these sequences within the MOMPs of all 15 C. trachomatis serovars. We used oligonucleotide primer extension sequencing of MOMP mRNA to determine the nucleotide and deduced amino acid sequences of the four MOMP VDs of the 15 C. trachomatis serovars. Comparative amino acid sequence homologies of all four domains separated the serovars into three groups: group 1, serovars B, Ba, D, E, L1, and L2; group 2, serovars G and F; and group 3, serovars A, C, H, I, J, K, and L3. Hydrophilicity and charge values for each domain were determined. The MOMP VDs of given serovars with the greatest total hydrophilicity and charge values were found to be the location of antigenic determinants recognized by MOMP-specific monoclonal antibodies. These findings should be useful for predicting MOMP antigenic determinants and testing the antigenic properties of these VDs by using synthetic peptides corresponding to each MOMP VD. The potential usefulness of the VD sequence information is discussed in relation to the development of defined synthetic peptides and oligonucleotides that may be used to develop new serological and diagnostic assays for C. trachomatis infections.

Organization of spliceosomal U6 snRNA genes in the mouse genome

U6 RNA is an abundant small nuclear RNA (snRNA) required for splicing of pre-mRNAs. In mammalian cells, the genes for U1 to U4 snRNAs consist of multigene families ranging from 10 to 100 copies of real genes per haploid genome, and are transcribed by RNA polymerase II. In contrast, results obtained in this study indicate that U6 RNA, which is transcribed by RNA polymerase II and III, may be coded for in mouse cells by only two genes. These two U6 genes are at least 9 kb apart from each other, and the flanking sequences are highly conserved, indicating that the organization of U6 genes is similar to that observed for other mammalian U-snRNA genes.

Changes in the rate of haemolysis during the early stage after burns in the rabbit

The kinetics of erythrocyte haemolysis in blood samples taken from normal and burned rabbits were investigated by nephelometry. The rate of haemolysis decreased significantly from 30 min to 2 h after severe burns, when many abnormal red cell forms were found in blood films; there was also an increase in osmotic fragility. The results confirm that the rate of haemolysis is strongly related to structural changes of the red cell membrane but do not parallel osmotic fragility. Differences in haemolysis rate and osmotic fragility between erythrocytes taken from burned animals and those heated in vitro suggest that erythrocyte changes following burning injury involve complex kinetic processes in which factors other than the direct effect of heat play important roles.

Distribution of red cell blood group systems in Yi, Tibetan and Manchu ethnic groups in China

A survey on distribution of ten red cell blood group systems was carried out in 1985 in the Yi, Tibetan and Manchu nationalities in China. Significant differences were found in the distribution of Rh, MNSs, P and especially in the ABO system, while no significant difference was found for Diego, Duffy, Kell, Kidd and XG systems. The DI*a gene frequency was about 0.03, FY*a rather high (0.94), KEL*K extremely low (0.005) and JK*a was about 0.4. In the three nationalities under study, Yi is characterized by high frequencies of the alleles A, M and CDe and by the absence of CDE and Cde. Tibetans show a high frequency of O and a relatively high frequency of P*P1, while Manchus have the lowest frequency of M and in particular of MS.

Rapid purification of arrowhead proteinase inhibitors by high performance hydrophobic interaction chromatography on a PEG bonded phase column

A new hydrophobic interaction HPLC column is used for the rapid purification of proteinase inhibitors isolated from arrowhead. The inhibitors, partially purified by DEAE-cellulose column chromatography, are resolved into three components with a mobile phase gradient of decreasing salt concentration from 1.1 M ammonium sulfate in 0.01 M phosphate buffer to phosphate buffer alone. This new HPLC column is found to be very useful for rapid, semipreparative purification of hydrophobic protein and sample loading of up to 1.6 mg of inhibitors can be fully resolved on an analytical column.