A non-metric sequence alignment program

An algorithm for nucleic acid and protein sequence alignment is presented. It is a non-metric local similarity minimal-difference algorithm and in the current implementation, assembles the matching regions found into a pseudo-global format. Its strengths are its speed of execution and the especially convenient presentation of its output. The algorithm is intended for use in sequence melding and local (small-region) similarity searching. It is not designed to replace a metric Needleman-Wunsch-Sellers-type similarity algorithm. The program is written in FORTRAN and is designed to be easily transportable to a variety of computer systems.     

A crustacean compound eye adapted for low light intensities (Isopoda)

Summary The optical performance of the apposition compound eye of the marine isopodCirolana borealis Lilljeborg (Crustacea) was investigated. The ommatidia comprise large lenses (diam. ca. 150 m), spherical crystalline cones and hypertrophied rhabdoms. The 7 rhabdomeres are fused distally and open proximally. We have designated this rhabdom type as semifused. Distal pigment cells screen neighbouring ommatidia, and a well developed reflecting pigment layer surrounds the rhabdom. The focal length was determined in situ and refractive index measurements, raytracings, and eye mappings were made. The focus was found to lie well below the distal rhabdom tip. A theoretical acceptance function was constructed and a 50% acceptance angle of 45 ° was estimated. The eye parameter (p, according to Snyder 1977) of different ommatidia was between 44 and 14. This together with the anatomy demonstrate an optimation to extremely low light intensities. TheCirolana eye provides an example where acuity is sacrificed for the eye to be able to see at the low light intensities of the inhabitat.The investigation has been supported by a grant from the Swedish Natural Science Research Council (grant no. 2760-103). Our thanks are due to the staff of the marine biological station in Espegrend (Norway). The skilled technical assistance of Miss Inger Norling, Mrs. Rita Wallen, and Miss Maria Walles is gratefully acknowledged. And finally, we would like to express our deep appreciation to Professor Rolf Elofsson for constructive discussions and for his interest and encouragement throughout the investigation.     

The identification of Tithonia voucher specimens used for sesquiterpene lactone investigations

The identification of Tithonia voucher specimens as T. rotundifolia (Mill.) Blake, used for sesquiterpene lactone chemical investigations, have been found to be T. diversifolia (Hemsl.) A. Gray. The compound Ivalin, also is reported for the first time from T. calva Sch. Bip. in Semann.     

A SURVEY FOR 1,3,6,7-TETRAHYDROXY-C-GLYCOSYLXANTHONES EMPHASIZING THE “PRIMITIVE” LEPTOSPORANGIATE FERNS AND THEIR ALLIES

A survey for 1,3,6,7-tetrahydroxy-C-glycosylxanthones of representative species within the primitive vascular plants, emphasizing the leptosporangiate ferns, has indicated a limited distribution of these compounds within three leptosporangiate families: Hymenophyllaceae, Aspleniaceae and Marsileaceae. In the Hymenophyllaceae the distribution of these compounds appears to be a useful criterion for segregating species of Mecodium from other species of Hymenophyllum (sensu lato) and suggests that the tubulate vs. the valvate indusial condition may not be an ideal character for separating all species of Hymenophyllum (s.l.) from those of Trichomanes (s.l.). These compounds appear useful for delimiting several species of Elaphoglossum section Pachyglossa and support a relationship among the Aspleniaceae, Athyriaceae, and Elaphoglossaceae. Their presence in Marsilea also raises questions as to the origin of this group of plants.     

Complementation between urokinase-producing and receptor-producing cells in extracellular matrix degradation.

The respective roles of urokinase plasminogen activator (u-PA) and the u-PA receptor in extracellular matrix degradation was investigated. Human pro-u-PA and the human u-PA receptor were expressed independently by two different mouse LB6 cell lines. The matrix degradation capacity of these cell lines individually or in coculture was studied. Although pro-u-PA-producing cells alone degrade the matrix in the presence of plasminogen, u-PA-receptor producing cells do not. Cocultivation of a small fraction of pro-u-PA-producing cells with the receptor-producing cells increases the rate of matrix degradation at least threefold. By immunoprecipitation it was shown that cocultivation of the two cell lines increases the conversion of the inactive pro-u-PA to the active two chain u-PA. The enhancement of matrix degradation and of pro-u-PA activation requires actual binding of pro-u-PA to its receptor because it is inhibited by u-PA-receptor antagonists. The u-PA receptor must be cell associated, as binding of pro-u-PA to a receptor solubilized from the cell surface with phosphatidyl-inositol specific phospholipase C did not enhance the activation of pro-u-PA in the presence of plasminogen. The finding that activity of u-PA is enhanced when it is bound to its receptor, even when the receptor is produced by a different cell, might have important implications for the mechanisms of u-PA-induced extracellular proteolysis in vivo.     

Nucleotide sequence of a cDNA from Onchocerca gibsoni encoding a novel repetitive antigen.

mRNA from uterine microfilariae of the cattle parasite Onchocerca gibsoni was used for the construction of cDNA libraries. A cDNA clone encoding an antigen recognized by serum from human individuals infected with O. volvulus was found to contain five copies of an 87 bp unit. These 87 bp units were present in the genome in high copy number as long tandem arrays. These are the first cDNA sequence data obtained directly from larvae of any Onchocerca species.     

Identification and characterization of the murine cell surface receptor for the urokinase-type plasminogen activator.

Cell-binding experiments have indicated that murine cells on their surface have specific binding sites for mouse urokinase-type plasminogen activator (u-PA). In contrast to the human system, chemical cross-linking studies with an iodinated ligand did not yield any covalent adducts in the murine system, but in ligand-blotting analysis, two mouse u-PA-binding proteins could be visualized. To confirm that these proteins are the murine counterpart of the human u-PA receptor (u-PAR), a peptide was derived from the murine cDNA clone assigned to represent the murine u-PAR due to cross-hybridization and pronounced sequence similarity with human u-PAR cDNA [Kristensen, P., Eriksen, J., Blasi, F. & Dan?, K. (1991) J. Cell Biol. 115, 1763-1771]. A rabbit antiserum raised against this peptide specifically recognized two polypeptide bands with electrophoretic mobilities identical to those identified by ligand-blotting analysis. Binding of mouse u-PA to its receptor showed species specificity in ligand-blotting analysis, since mouse u-PA did not bind to human u-PAR and human u-PA did not bind to mouse u-PAR. The apparent M(r) of mouse u-PAR varied between different mouse cell lines and ranged over M(r) 45,000-60,000. In four of the cell lines, mouse u-PA bound to two mouse u-PAR variant proteins, whereas in the other two cell lines studied, there was only one mouse u-PA-binding protein. In the monocyte macrophage cell line P388D.1, trypsin-treatment of intact cells could remove only the large mouse u-PAR variant (M(r) 60,000) indicating that only this type was a cell-surface-exposed molecule. The smaller mouse u-PAR variant (M(r) 45,000), was deglycosylated by the enzyme endo-beta-N-acetylglucosaminidase H and is probably an intracellular precursor form carrying only high-mannose carbohydrate. Deglycosylation of this variant yielded a polypeptide with an apparent M(r) of about 30,000, which corresponds to the Mr calculated from the cDNA derived protein sequence of mouse u-PAR. Receptor-bound mouse u-PA could be released by phosphatidylinositol-specific phospholipase C treatment, indicating that mouse u-PAR is attached to the cell surface by glycosylphosphatidylinositol. Purification of the two mouse u-PAR variant proteins by diisopropylfluorophosphate-inactivated mouse u-PA-Sepharose affinity chromatography yielded two silver-stained bands when analysed by SDS/PAGE, corresponding in electrophoretic mobility to those seen by ligand-blotting analysis.(ABSTRACT TRUNCATED AT 400 WORDS)