Gene structure prediction by linguistic methods

The higher-order structure of genes and other features of biological sequences can be described by means of formal grammars. These grammars can then be used by general-purpose parsers to detect and to assemble such structures by means of syntactic pattern recognition. We describe a grammar and parser for eukaryotic protein-encoding genes, which by some measures is as effective as current connectionist and combinatorial algorithms in predicting gene structures for sequence database entries. Parameters of the grammar rules are optimized for several different species, and mixing experiments are performed to determine the degree of species specificity and the relative importance of compositional, signal-based, and syntactic components in gene prediction.

Gamma and delta chain gene rearrangement of T cell receptor in acute lymphoblastic leukemia

The immunophenotype, rearrangements of T cell receptor (TCR) gamma and delta chain genes as well as the immunoglobulin heavy chain (IgH) gene were studied in 37 cases of morphologically defined acute lymphoblastic leukemia (ALL). According to the expression of differentiation antigens, 8 cases were classified as T-ALL, 26 B lineage ALL, 2 acute undifferentiated leukemia (AUL) and myeloid phenotype. An order of TCR gene rearrangements was observed in T-ALL, with the rearrangement of delta gene preceding that of gamma gene. Both genes were also found frequently rearranged and/or deleted in high proportions of the ALL of B cell lineage. However, the patterns of gene rearrangements were somewhat different between the T and B lineage ALLs. In contrast, the IgH gene rearrangements were observed only in the B lineage ALL. The immunogenotype analysis of ALL proved to be a useful marker of the clonality and provided us with important information on early human lymphoid differentiation. We conclude that the determination of TCR gamma gene V-J junctional sequence can be used as clonal marker for detecting the minimal residual disease during clinical remission.

Performance of a 2.3-kW Nd:YAG slab laser system

A slab laser system consisting of three Nd:YAG slabs with dimensions 7 mm x 26 mm x 191 mm was operated with different resonators in an oscillator-amplifier-amplifier arrangement. In single-shot operation the system provided a maximum output energy of 148 J with a pulse duration of 4 ms and an overall efficiency of 4.3%. A stable resonator provided a maximum steady output power of 2260 W, and we measured beam parameter products of 8 mm mrad in the x direction and 100 mm mrad in the y direction. An output power of 1460 W and beam parameter products of less than 4 mm mrad in both directions were obtained with an unstable resonator with a graded-reflectivity mirror.

Identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus

The murine coronavirus mouse hepatitis virus gene 1 is expressed as a polyprotein, which is cleaved into multiple proteins posttranslationally. One of the proteins is p28, which represents the amino-terminal portion of the polyprotein and is presumably generated by the activity of an autoproteinase domain of the polyprotein (S. C. Baker, C. K. Shieh, L. H. Soe, M.-F. Chang, D. M. Vannier, and M. M. C. Lai, J. Virol. 63:3693-3699, 1989). In this study, the boundaries and the critical amino acid residues of this putative proteinase domain were characterized by deletion analysis and site-directed mutagenesis. Proteinase activity was monitored by examining the generation of p28 during in vitro translation in rabbit reticulocyte lysates. Deletion analysis defined the proteinase domain to be within the sequences encoded from the 3.6- to 4.4-kb region from the 5' end of the genome. A 0.7-kb region between the substrate (p28) and proteinase domain could be deleted without affecting the proteolytic cleavage. However, a larger deletion (1.6 kb) resulted in the loss of proteinase activity, suggesting the importance of spacing sequences between proteinase and substrate. Computer-assisted analysis of the amino acid sequence of the proteinase domain identified potential catalytic cysteine and histidine residues in a stretch of sequence distantly related to papain-like cysteine proteinases. The role of these putative catalytic residues in the proteinase activity was studied by site-specific mutagenesis. Mutations of Cys-1137 or His-1288 led to a complete loss of proteinase activity, implicating these residues as essential for the catalytic activity. In contrast, most mutations of His-1317 or Cys-1172 had no or only minor effects on proteinase activity. This study establishes that mouse hepatitis virus gene 1 encodes a proteinase domain, in the region from 3.6 to 4.4 kb from the 5' end of the genome, which resembles members of the papain family of cysteine proteinases and that this proteinase domain is responsible for the cleavage of the N-terminal peptide.

Molecular study on the chromosome 15 breakpoints in the translocation t(15; 17) in acute promyelocytic leukemia (APL)

Chromosomal translocation t(15; 17) is a specific marker of acute promyelocytic leukemia (APL). In this study, molecular cloning of the t(15; 17) breakpoint was carried out in a Chinese APL patient. It has been shown that the retinoic acid receptor alpha (RARA) gene, normally located on chromosome 17, was fused with a new transcription unit PML, normally localized on chromosome 15. We have subsequently cloned a portion of the PML gene and generated a panel of probes. A PML gene rearrangement was detected in 33 out of 36 APL cases studied. 24 rearrangements were clustered in a 4.4 kb region, designated here as PMLbcr1 whereas 9 rearrangements were concentrated in a 6.5 kb region, defining another breakpoint cluster region (PMLbcr2). These two types of rearrangement constitute the basis for the heterogeneity of the PML-RARA fusion gene and its possible biological significance remains to be explored.

Breakpoint clusters of the PML gene in acute promyelocytic leukemia: primary structure of the reciprocal products of the PML-RARA gene in a patient with t(15;17)

DNA studies of the translocation t(15;17) in acute promyelocytic leukemia (APL) have shown that the retinoic acid receptor alpha (RARA) gene on chromosome 17 is juxtaposed to the promyelocytic leukemia (PML) gene on chromosome 15. The PML breakpoints have been mapped to 3 clusters: bcr1, bcr2, and bcr3. We have examined the PML breakpoint distribution in a series of 33 Chinese patients with APL. Twenty-two patients fell within bcr1, 2 within bcr2, and 9 within bcr3. The primary structure of the reciprocal chromosome translocation joints of one patient and that of their normal counterparts have been determined and compared to those of 2 previously reported cases. These studies revealed possible topoisomerase II cleavage sites close to the breakpoints and suggested implications of DNA attachment sites to nuclear matrix. We propose that these features are relevant to the process of illegitimate recombination generating the translocation.

Localization of the chromosome 15 breakpoints and expression of multiple PML-RAR alpha transcripts in acute promyelocytic leukemia: a study of 28 Chinese patients

Translocation (15;17)(q22;q12-q21) is a chromosome aberration specifically found in acute promyelocytic leukemia (APL), that generates a chimeric gene between the promyelocytic leukemia (PML) gene on chromosome 15 and the retinoic acid receptor alpha (RARA) gene, on chromosome 17. In the course of molecular investigations of a series of 28 Chinese patients with APL, we have simultaneously used Southern blot and reverse transcriptase polymerase chain reaction (RT-PCR) analysis to characterize the PML gene breakpoints on chromosome 15 and identify PML-RARA fusion transcripts. Our results confirmed the existence of the three recently described bcr1, bcr2, and bcr3 breakpoint cluster regions. In addition, structural data provided by PML-RARA transcripts allowed us to more accurately locate the 3' borders of clusters bcr1 and bcr3. Moreover, our data suggest a preferential localization of the breakpoints within bcr1 and bcr3. The primary structure of a 1.4 kb DNA segment flanking the 5' part of the PML gene and that of the bcr3 cluster (2.1 kb) were also established.

Occurrence of distinct PML-RAR-alpha fusion gene isoforms in patients with acute promyelocytic leukemia detected by reverse transcriptase/polymerase chain reaction

A specific 'nested' reverse transcriptase/polymerase chain reaction (RT/PCR) procedure was used to characterize the expression patterns of PML-RAR-alpha chimeric mRNAs in 32 patients with acute promyelocytic leukemia (APL). The sensitivity of the technique was such that the fusion gene transcript could be detected from as little as 2.5 pg of total leukemic cell RNA against a background of 1 microgram of cellular RNA lacking the PML-RAR-alpha fusion gene transcript(s). In 19 cases the PML-RAR-alpha isoform referred to here as long was identified. A short isoform, which in comparison with the long form lacks three PML exons, was detected in 11 other cases. A third PML-RAR-alpha mRNA isoform, in which the most 3' PML exon present in the long-type isoform was truncated in its sequences lying immediately upstream of RAR-alpha B region, was found and characterized in a single patient. In one APL patient with a variant translocation t(11;17), the PCR product corresponding to PML-RAR-alpha chimeric mRNAs could not be amplified despite the presence of RAR-alpha gene rearrangement. Genomic and PCR analysis showed that the different PML-RAR-alpha isoforms found in APL patients arise as a result of distinct translocation breakpoints. In each case the exons encoding the B-F regions of RAR-alpha are expressed and are spliced downstream from variable PML gene exons. The 'nested' RT/PCR analysis of the PML-RAR-alpha fusion gene proved to be a rapid and sensitive tool for the diagnosis of the APL and for monitoring the residual APL chimeric mRNA expression during complete remission.

Molecular rearrangements of the MYL gene in acute promyelocytic leukemia (APL, M3) define a breakpoint cluster region as well as some molecular variants

Genomic DNA probes generated from the retinoic acid receptor alpha (RARA) gene located on chromosome 17 and from the MYL gene located on chromosome 15 were used to study the chromosome 15 breakpoints resulting from the t(15; 17) translocation in 26 patients with acute promyelocytic leukemia (APL). In 20 out of 22 patients with a detectable MYL rearrangement, the breakpoints were clustered within a 4.4 kb segment designated MYLbcr. The two remaining patients exhibited a more 5' rearrangement at about 10 kb upstream of the MYLbcr region, implying the lack of at least one MYL gene exon in the resulting MYL-RARA fusion gene. The variation of chromosome breakpoints within the MYL gene may explain size heterogeneity previously observed in some MYL-RARA fusion transcripts expressed in APL cells.

Rearrangements in the second intron of the RARA gene are present in a large majority of patients with acute promyelocytic leukemia and are used as molecular marker for retinoic acid-induced leukemic cell differentiation

Chromosome 17 breakpoints in translocation t(15;17), a hallmark for acute promyelocytic leukemia (APL), have been shown to disrupt the retinoic acid receptor-alpha (RARA) gene. In this study, DNA probes around the second exon of the RARA gene showed rearrangements not previously detected. Analysis of 25 Chinese APL cases showed that RARA gene rearrangements were present in 23 cases (92%). The breakpoints were mapped unequivocally in 22 cases within the second intron of the gene. Therefore, the RARA gene rearrangement provides us with a specific marker of the disease. Simultaneous molecular and cytologic studies showed that the RARA gene rearrangements persisted during the first 2 to 3 weeks of all-trans retinoic acid (ATRA) therapy when differentiated granulocytes predominated in bone marrow, while these rearrangements disappeared after achieving complete remission. These data indicate that ATRA induces differentiation of APL cells.

[Chromosome polymorphism in five hydatidiform moles]

Five hydatidiform moles were karyotyped and their genetic origins were investigated using chromosome polymorphisms. 4 cases of complete mole were diploid, homozygous, female, androgenetic in origin. 1 case of partial mole was triploid, 69, XXY and with a chromosomal contribution from the female gamete.

Treatment of 910 cases of atrophic gastritis with wei you decoction

In treatment of 910 cases of chronic atrophic gastritis with Wei You Decoction, the overall effective rate was 96.9%. The disease was considered as due to deficiency of vital energy with stagnation of cold, and therefore treatment was to invigorate blood circulation. The Wei You Decoction had functions of replenishing vital energy, warming the middle burner, invigorating blood circulation, and resolving stasis, thus reversing the morbid process in the gastric mucosa. It was nontoxic, and the side-effects were minimal. The therapeutic effect was prompt and persistent. No malignant change was observed after taking the drug.

[Discrimination between fructus Foeniculi and fructus Anethi by cellulose acetate membrane electrophoresis]

The discrimination between Fructus Foeniculi and Fructus Anethi was studied by cellulose acetate membrane electrophoretic method. The two drugs can be easily distinguished from each other in terms of the band number and colour of the electrophoretograms of the water soluble proteins.

The effects of caffeine on the ultrastructure and mitochondrial function of the embryonic chick heart

Results from this study indicate that caffeine (at an embryotoxic dose equal to the LD40 administered to 3-day chick embryos produced both ultrastructural and functional abnormalities in embryonic cardiac mitochondria. The principal effects of caffeine on the ultrastructure of embryonic myocardial cells were clearly suggestive of cellular injury and included: (1) a marked disruption of mitochondrial cristae with formation of intramitochondrial myelin-like figures and (2) intracellular edema. A biochemical analysis of mitochondrial function revealed that caffeine inhibited the capacity of mitochondria to oxidize succinate. However, when pyruvate and malate were employed as substrates for isolated mitochondria, caffeine did not significantly alter mitochondrial function. Interference with embryonic cardiac mitochondrial succinate oxidation and/or fragmentation of mitochondrial membranes are suggested as possible events in the pathogenesis of caffeine-induced cardiac cell injury which, in turn, may lead to the embryonic death of the chick.

Kinetics of unfolding of proteins on hydrophobic surfaces in reversed-phase liquid chromatography

As a continuation of previous studies, we present in this paper measurements on the kinetics of denaturation of papain, soybean trypsin inhibitor and lysozyme on n-butyl-bonded silica gel surfaces used in reversed-phase liquid chromatography (RPLC). In all cases, native and denatured peaks widely separated from one another are observed. The rate constants for denaturation or unfolding are determined by the measurement of the peak area of the native protein as a function of the incubation time that the species spends on the bonded-phase surface. The results reveal that a slow denaturation step occurs with a half-life of ca. 15 min. In addition, studies of denaturation as a function of the amount of 1-propanol in the initial mobile phase suggest an additional unfolding step when the protein comes in contact with the bonded-phase surface. The extent of this latter step decreases as the concentration of 1-propanol increases, further suggesting that 1-propanol sorption on the bonded stationary phase may play a role in this behavior. Other studies are conducted with alpha-chymotrypsinogen, in which injection is made after the start of the gradient. The extent of denaturation is observed to be a function of the organic modifier employed. The results of this paper provide insight into the denaturation process in RPLC and suggest approaches to minimize this behavior.

Congenital blood cysts of the heart valves

Congenital blood cysts of the heart valves are found most commonly on the tricuspid and mitral valves of fetuses and infants. Hearts available following 38 random autopsies of fetuses and infants 2 years of age or younger were examined. Blood cysts were found in 18 cases (47 per cent) in which ages ranged from 26 weeks of gestation to 11 months. The cysts varied in diameter, from microscopic to 3 mm. Affected valves had from one to 20 cysts. Light microscopic examination of serially sectioned paraffin-embedded tissue and plastic-embedded tissue and scanning electron microscopic examination revealed connections between the cyst lumens and ventricles via small endothelium-lined channels. The cyst structure suggested formation from ventricular endothelial infoldings in the valve leaflet base, which bulged into the atrium because of the pressure gradient present during valve closure. Blood cysts are a common finding in neonates dying of various causes and probably have no clinical significance. There is no association with asphyxia as previously described. Blood cysts may persist and enlarge to form giant cysts of the heart valves.

Glomerular accumulation of monocytes and macrophages in experimental glomerulonephritis associated with Trypanosoma rhodesiense infection

Experimental infection in rabbits with a human isolate of Trypanosoma rhodesiense led to the formation of circulating immune complexes and glomerulonephritis. Granular deposits of C3 and lesser amounts of IgM and IgG were seen deposited in the glomeruli in a primarily mesangial pattern. The glomeruli became hypercellular beginning on day 7. This was associated with diffuse swelling and vacuolation of endothelial cells with focal loss of fenestrae, as well as vacuolation of mesangial cells processes protruding into the capillary lumina. The hypercellularity became maximal on day 21 and was accompanied by proteinuria and increased tubular hyaline droplets. The hypercellularity was in large part due to the accumulation of monocytes as demonstrated by nonspecific cytoplasmic esterase stains. Counts of the number of monocytic cellular profiles per glomerulus showed that maximal numbers were reached on the 21st day of the infection. Ultrastructural examination confirmed the presence of monocytes within capillary lumina and macrophages within mesangial regions. Electron-dense deposits were rarely seen by transmission electron microscopy, and the heavy granular deposits of IgM and C3 observed by immunofluorescence were attributed to ingested proteins within macrophages. This study implies an active role for monocytes and macrophages in immune complex-mediated glomerulonephritis.

The ultrastructure of the thin limbs of Henle in Kidneys of the desert heteromyid (Perognathus penicillatus)

The thin limbs of both long- and short-looped nephrons in Perognathus kidneys were studied with transmission and scanning electron microscopy. The superficial nephrons have a short thin limb located in the vascular bundles of the outer medulla and are characterized by a simple, low-lying epithelium (0.4 +/- 0.1 mu thickness). In contrast, the first descending part of the thin limb of the majority of midcortical and juxtamedullary nephrons has a relatively thick epithelium (1.7 +/- 0.6 mu in thickness) with marked lateral and basal interdigitation and a dense surface covering of microvilli. The remaining part of the long descending thin limb is relatively simple with a low-lying epithelium (0.6 +/- 0.1 mu in thickness), decorated on its surface by sparse microplicae. The bend of the loop and the ascending limb are covered by a very simple low-lying epithelium (0.6 +/- 0.2 mu in thickness) with relatively little surface modification. The extreme urine-concentrating ability of Perognathus does not appear to be due to the development of a unique thin loop epithelium but rather to the extensive length of the inner and outer medulla.

Pathology of experimental African trypanosomiasis in rabbits infected with Trypanosoma rhodesiense

The pathologic response of New Zealand White rabbits to experimental infection with Trypanosoma rhodesiense is described. Autopsies of 18 rabbits killed from 30-44 days after infection revealed focal perivascular inflammation of the ears, eyes and testes. Examination by electron microscopy revealed extravascular trypanosomes in the dermis of the ear and interstitium of testes. Deposits of IgG, IgM and C3 were in renal glomeruli associated with glomerular hypercellularity; proteinuria was present as evidenced by an increase in tubular hyaline droplets. There was marked hyperplasia of lymph nodes and spleen with generalized increase in the number of macrophage and plasma cells. In contrast there was thymic atrophy. The findings suggest an immunologic host response associated with severe localized vascular injury.

Values for tissue magnesium as a guide in detecting magnesium deficiency

A large-scale survey of the normal magnesium content of various human tissues was carried out to facilitate clinical detection of magnesium deficiency, especially occult deficiency.A review of the literature favours the magnesium content of skeletal muscle as the most reliable index of the body's store of magnesium. There is a significant difference (P < 0.001) in both the serum and erythrocyte magnesium levels between normal pregnant women in the third trimester and the average normal population. The reason for this difference is discussed.