A computer algorithm to determine the recognition site of restriction enzymes

A new algorithm is proposed to determine the type-II restrictionendonucleases' recognition site knowing the digested DNA sequenceand fragment lengths in an actual case. The algorithm is implementedfor the Commodore 64 microcomputer. Received on January 6, 1987; accepted on June 19, 1987     

Origin of the genetic code: A physical-chemical model of primitive codon assignments

Selective compartmentalization of amino acids and nucleotides according to their polarities is proposed as a physical-chemical model for the origin of the genetic code. Assumptions made in this hypothesis are: (1) an oil-slick covered the surface of the primitive ocean, constituents of which formed association colloids or micelles at the water-oil-air interfaces; (2) depending on the polarity of the media, these aggregates possessed hydrophilic and hydrophobic interiors where selective uptake of amino acids and nucleic acid constituents could take place; and 93) condensation and polymerization in the micellar phase were enhanced. According to the chromatographically observed polarities, for example, lysine and uridylate fall into the hydrophilic compartment, and phenylalanine and adenylate are enriched in the hydrophobic environment. These components could eventually be condensed to form a charged adaptor loop with an anticodon which is complementary to the presently valid codon. Only two groups of amino acids, hydrophilic and hydrophobic, were recognized by the primitive translation mechanism. Implications of this hypothesis for the further development of the genetic code is discussed. The catalytic power of micelles have been substantiated by successful synthesis of nucleotides under relatively mild conditions using thiophosphates as high energy phosphates.     

THE STRUCTURE AND FUNCTION OF CENTRIOLES AND THEIR SATELLITES IN THE JELLYFISH PHIALIDIUM GREGARIUM

Testes of jellyfish Phialidium gregarium were fixed in 2 per cent OsO₄ in Veronal-acetate buffer at pH 7.4. Thin sections showed that in young spermatids the spindle fibers of the last maturation division are attached to satellites of the filament-forming centriole. In more mature spermatids this attachment is not observed. During the developmental phase, nine satellites can be observed emanating from the interspaces between the nine tubular triplets of this centriole. A circular region on each of the enlarged distal ends of the satellites attaches them to the cell membrane. The satellites apparently provide a firm anchor for the axial filament. Each of the epithelial cells covering the testis produces a single long flagellum. On the filament-forming centriole often a satellite can be observed to which tubules are attached. These tubules are 180 A in diameter and probably represent remnants of spindle fibers. It is suggested that the distal centriole has the ability to form several satellites or appendages at appropriate times during the cell cycle. These satellites are distinct from the daughter centrioles in that they are supportive structures: in certain phases of cell life, spindle fibers may attach to them, while in other instances the distal centriole and the flagellum it is forming are anchored by them.     

EXTRUSION OF NUCLEOLI FROM PRONUCLEI OF THE RAT

Electron microscope observations of osmium tetroxide-fixed rat eggs indicate that small nucleoli are extruded from pronuclei in a sharply demarcated time period after sperm penetration. Approximately 4½ hours after sperm penetration, fine fibrous material aggregated in distinct loci along the inner surface of the nuclear envelope and condensed into small, dense bodies. The term tertiary nucleolus or extrusion body is used to designate the forming bodies. The small tertiary nucleoli form distinct protrusions from the pronuclei during the following developmental period and finally bud off into the cytoplasm, carrying with them a small portion of the double nuclear envelope. The extrusion bodies can be observed only in the vicinity of the pronuclei and have not been seen near the cell membrane. The fate of the tertiary nucleoli is not known; apparently they transform or disappear after they have passed into the cytoplasm. Eleven hours after sperm penetration, tertiary nucleoli are not present near the nuclear membrane and the extrusion activity has apparently ceased. Large and small nucleoli react similarly to cytochemical reagents: they are Feulgen negative; they are positive to the Millon, Sakaguchi, brom-phenol blue, and PAS reactions. Azure B stain combined with nuclease extraction indicates the presence of small amounts of RNA in the nucleoli.     

OBSERVATIONS ON SPERM PENETRATION IN THE RAT

The structural aspects of sperm penetration in the rat egg were investigated by electron microscopy. Eggs were recovered at intervals between 8 and 10:30 A.M. from females which had mated during the previous night. The oviducts were flushed with hyaluronidase and the eggs transferred into a 2 per cent osmium tetroxide solution, buffered at pH 7.8. After fixation, the eggs were mounted individually in agar, dehydrated in ethyl alcohol, and embedded in butyl-methyl methacrylate (3:1). The sperm penetrating the egg is covered by a plasma membrane which is present only on the side facing toward the zona pellucida; no membrane is visible on the side facing toward the vitellus. The sperm plasma membrane becomes continuous with the egg plasma membrane and forms a deep fold around the entering sperm. Cross-sections through the sperm midpiece in the perivitelline space show an intact plasma membrane. At the place of entrance, the plasma membrane of the sperm appears to fuse with the egg plasma membrane. After the sperm has penetrated the vitellus, it has no plasma membrane at all. The nuclear membrane is also absent. These observations suggest a new hypothesis for sperm penetration. After the sperm has come to lie on the plasma membrane of the egg, the egg and sperm plasma membranes rupture and then fuse with one another to form a continuous cell membrane over the egg and the outer surface of the sperm. As a result the sperm comes to lie inside the vitellus, leaving its own plasma membrane incorporated into the egg membrane at the surface of the egg.     

Studies on epimerization-free methods for the preparation of aminosuccinyl peptides

Summary We have found that guanidine acetate catalyses the transformation of a -benzyl-aspartyl peptide (Boc-Asp-(OBzl)-Leu-Trp-OMe) to an aminosuccinyl peptide (Boc-Asu-Leu-Trp-OMe). The reaction was accompanied by partial epimerization. However, not even a small amount of epimerization could be detected when the aminosuccinyl peptide was synthesised from Boc-Asp-Leu-Trp-OMe with the addition of DIC, HOPfp and guanidine acetate (as a catalyst). This reaction seems to be suitable for the epimerization-free solid phase synthesis of aminosuccinyl peptides, e.g. Asu⁶-Lamprey-III-GnRH (Glp-His-Trp-Ser-His-Asu-Trp-Lys-Pro-Gly-NH₂).     

Light-driven primary sodium ion transport in halobacterium halobium membranes

Light-induced sodium extrusion from H halobium cell envelope vesicles proceeds largely through an uncoupler-sensitive pathway involving bacteriorhodopsin and a proton/sodium antiporter. Vesicles from bacteriorhodopsin-negative strains also extrude sodium ions during illumination, but this transport is not sensitive to uncouplers and has been proposed to involve a light-energized primary sodium pump. Proton uptake in such vesicles is passive, and under steady-state illumination the large electrical potential (negative inside) is just balanced by a pH difference (acid inside), so that the protonmotive force is near zero. Action spectra indicated that this effect of illumination is attributable to a pigment absorbing near 585 nm (of 568 for bacteriorhodopsin). Bleaching of the vesicles by prolonged illumination with hydroxylamine results in inactivation of the transport; retinal addition causes partial return of the activity. Retinal addition also causes the appearance of an absorption peak at 588 nm, while the absorption of free retinal decreases. The 588 nm pigment is present in very small quantities (0.13 nmole/mg protein), and behaves differently from bacteriorhodopsin in a number of respects. Vesicles can be prepared from bacteriorhodopsin-containing H halobium strains in which primary transport for both protons and sodium can be observed. Both pumps appear to cause the outward transport of the cations. The observations indicate the existence of a second retinal protein, in addition to bacteriorhodopsin, in H halobium, which is associated with primary sodium translocation. The initial proton uptake normally observed during illumination of whole H halobium cells may therefore be a passive flux in response to the primary sodium extrusion.     

Activated p53 in the anti-apoptotic milieu of tuberous sclerosis gene mutation induced diseases leads to cell death if thioredoxin reductase is inhibited

Apoptosis - Tuberous sclerosis, angiomyolipoma and lymphangioleiomyomatosis are a group of diseases characterized by mutation in tuberous sclerosis genes (TSC 1-2). TSC mutation leads to continuous...     

A Novel Source of Cultured Podocytes

Amniotic fluid is in continuity with multiple developing organ systems, including the kidney. Committed, but still stem-like cells from these organs may thus appear in amniotic fluid. We report having established for the first time a stem-like cell population derived from human amniotic fluid and possessing characteristics of podocyte precursors. Using a method of triple positive selection we obtained a population of cells (hAKPC-P) that can be propagated in vitro for many passages without immortalization or genetic manipulation. Under specific culture conditions, these cells can be differentiated to mature podocytes. In this work we compared these cells with conditionally immortalized podocytes, the current gold standard for in vitro studies. After in vitro differentiation, both cell lines have similar expression of the major podocyte proteins, such as nephrin and type IV collagen, that are characteristic of mature functional podocytes. In addition, differentiated hAKPC-P respond to angiotensin II and the podocyte toxin, puromycin aminonucleoside, in a way typical of podocytes. In contrast to immortalized cells, hAKPC-P have a more nearly normal cell cycle regulation and a pronounced developmental pattern of specific protein expression, suggesting their suitability for studies of podocyte development for the first time in vitro. These novel progenitor cells appear to have several distinct advantages for studies of podocyte cell biology and potentially for translational therapies.