Intron positions correlate with module boundaries in ancient proteins.

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of "linker regions" that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions.

Technetium Tc 99m rapidly crosses the ovine placenta and intramembranous pathway.

Objective: This study examined the movement of the soluble ion technetium Tc 99m across the ovine placenta and intramembranous pathway.

Study Design: Nineteen fetal sheep at 131 +/- 1 (SE) days' gestation were studied. After a 1-hour control period technetium Tc 99m was injected into either a fetal vein (n = 7), the amniotic cavity (n = 5), or a maternal vein (n = 5).

Novel Gq alpha isoform is a candidate transducer of rhodopsin signaling in a Drosophila testes-autonomous pacemaker.

DGq is the alpha subunit of the heterotrimeric GTPase (G alpha), which couples rhodopsin to phospholipase C in Drosophila vision. We have uncovered three duplicated exons in dgq by scanning the GenBank data base for unrecognized coding sequences. These alternative exons encode sites involved in GTPase activity and G beta-binding, NorpA (phospholipase C)-binding, and rhodopsin-binding.

Active transposition in zebrafish.

We have identified a new family of Tc1-like transposons in the zebrafish, Danio rerio. The sequence of a candidate active transposon, deduced from sample Tzf elements, shows limited resemblance to the previously described Tdr1 elements of zebrafish. Both the Tzf and the Tdr elements are extremely abundant in zebrafish.

Partial retinal detachment at 3 months after threshold retinopathy of prematurity. Long-term structural and functional outcome. Multicenter Trial of Cryotherapy for Retinopathy of Prematurity Cooperative Group.

Objective: To investigate the structural and functional outcome at age 4 1/2 years of eyes that had partial retinal detachment (RD) at 3 months after the occurrence of threshold retinopathy of prematurity; these eyes were involved in the Multicenter Trial of Cryotherapy for Retinopathy of Prematurity study.

Methods: Of the 531 eyes in the randomized portion of the Multicenter Trial of Cryotherapy for Retinopathy of Prematurity study, 61 had partial RD at the 3-month examination. The extent of retinal involvement was recorded, and the presence of a foveal detachment was noted.

Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.

Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although exon shuffling in plants has been inferred from the analysis of intron phases of plant genes [Long, M., Rosenberg, C.

Introns and gene evolution.

In one scenario of gene evolution, exon shuffling has a fundamental role in increasing gene diversity. As DNA sequences accumulate in the databases, the picture of the intron/exon structures of genes becomes more and more clear. We discuss in this review some features of this picture that suggest that introns have been present since the early stages of evolution, and that exon shuffling was a fundamental process in the construction of ancient as well as modern genes.

Discovery of amphibian Tc1-like transposon families.

We have discovered transposase sequences in the bull frog (Rana catesbeiana) and in the clawed frog (Xenopus laevis), which demonstrates that there are DNA-mediated transposons in Amphibia. The DNA sequences of 11 new Xenopus elements describe two new vertebrate transposon families. Phylogenetic analysis, using these sequences along with previously defined vertebrate and invertebrate elements, reveals at least five families of Tc1-like elements in Vertebrata.

Early retinal vessel development and iris vessel dilatation as factors in retinopathy of prematurity. Cryotherapy for Retinopathy of Prematurity (CRYO-ROP) Cooperative Group.

Objective: To determine whether the extent of retinal vessel development present on early screening examinations for retinopathy of prematurity has prognostic value?

Design: The prospectively collected data from the Multicenter Trial of Cryotherapy for Retinopathy of Prematurity were used to compare the development of acute retinopathy of prematurity and long-term structural and visual outcomes for eyes with differing extents of retinal vessel development.

Patient: Study patients had eyes with the following vessel development. In zone I eyes, vessels extended from the disc less than twice the distance from the disc to the macula.

Intron phase correlations and the evolution of the intron/exon structure of genes.

Two issues in the evolution of the intron/exon structure of genes are the role of exon shuffling and the origin of introns. Using a large data base of eukaryotic intron-containing genes, we have found that there are correlations between intron phases leading to an excess of symmetric exons and symmetric exon sets. We interpret these excesses as manifestations of exon shuffling and make a conservative estimate that at least 19% of the exons in the data base were involved in exon shuffling, suggesting an important role for exon shuffling in evolution.

Evolution of the intron-exon structure of eukaryotic genes.

The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of introns', debate the presence or absence of introns in primordial genes. Both sides of the argument have focused on the positions of introns with respect to protein and gene structures.

Retinoic acid in the anteroposterior patterning of the zebrafish trunk.

Retinoic acid has been linked to pattern formation in the vertebrate anteroposterior axis. This report describes the spatial and temporal distributions of both endogenous retinoic acid and retinoic acid synthase activity along the anteroposterior axis of neurulating zebrafish embryos, as detected by a transient transgenic assay and by a zymography bioassay. Both retinoic acid levels and synthase activity were found to be highest in anterior regions of the trunk at all of the stages which were analysed.

Changes in blood flow to the ovine chorion and amnion across gestation.

Objective: The purpose of this study was to determine the developmental changes in blood flow to the network of fetal microvessels in ovine chorion and amnion.

Methods: Colored microspheres (15.10 +/- 0.

A novel yeast gene product, G4p1, with a specific affinity for quadruplex nucleic acids.

G4 nucleic acids are four-stranded helical structures that are formed in vitro by nucleic acids that contain guanine tracts. These structures anneal readily under physiological conditions and are unusually stable once formed. G4 nucleic acids are thought to participate in telomere function, retroviral genome dimerization, chromosome alignment during homologue pairing, and mitotic recombination, although the in vivo demonstration of these structures in any of these situations has not yet been achieved.

Large-scale genomic sequencing: optimization of genomic chemical sequencing reactions.

We have developed a streamlined, reproducible method for performing genomic chemical sequencing reactions on the genomic DNA of Mycoplasma capricolum, which has a genome size of about 750,000 base pairs and whose composition is 75% AT. The general modifications that ensure reproducibility and allow the processing of multiple samples can be widely adopted to other large-scale sequencing projects, while the specific modifications to the chemical reactions are applicable to the sequencing of other DNAs with a high AT content.

Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening.

The yeast gene KEM1 (also named SEP1/DST2/XRN1/RAR5) produces a G4-DNA-dependent nuclease that binds to G4 tetraplex DNA structure and cuts in a single-stranded region 5' to the G4 structure. G4-DNA generated from yeast telomeric oligonucleotides competitively inhibits the cleavage reaction, suggesting that this enzyme may interact with yeast telomeres in vivo. Homozygous deletions of the KEM1 gene in yeast block meiosis at the pachytene stage, which is consistent with the hypothesis that G4 tetraplex DNA may be involved in homologous chromosome pairing during meiosis.

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.

We report on the analysis of 214kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the estimated total number of 500 predicted for this organism. A large fraction of these (75%) can be assigned a likely function as a result of similarity searches.

Absence of polymorphism at the ZFY locus on the human Y chromosome.

DNA polymorphism in the Y chromosome, examined at a 729-base pair intron located immediately upstream of the ZFY zinc-finger exon, revealed no sequence variation in a worldwide sample of 38 human males. This finding cannot be explained by global constraint on the intron sequence, because interspecific comparisons with other nonhuman primates revealed phylogenetically informative sequence changes. The invariance likely results from either a recent selective sweep, a recent origin for modern Homo sapiens, recurrent male population bottlenecks, or historically small effective male population sizes.

Potential route for fetal therapy: intramembranous absorption of intraamniotically injected furosemide.

Objective: Our purpose was to determine whether intraamniotically injected furosemide could be absorbed directly into fetal circulation by the ovine intramembranous pathway.

Study Design: Nine chronically catheterized fetal sheep, five with an intact and four with a surgically ligated esophagus, were studied for 7 hours on 2 consecutive days. Day 1 was a control day in which the fetal parameters of arterial, venous, and amniotic fluid pressures; heart rate; and urine flow were measured continuously.

A yeast gene product, G4p2, with a specific affinity for quadruplex nucleic acids.

G4 nucleic acids are quadruplex structures involving guanine-rich sequences that form in vitro under moderate conditions. Experimental evidence exists supporting biological functions for these elements; however, direct demonstration of G4 nucleic acids in vivo has not yet been achieved. Here we purify and characterize a yeast protein, G4p2, which has a specific affinity for G4 nucleic acids.

The genetic data environment an expandable GUI for multiple sequence analysis.

An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC workstations. There is no limitation to the number of external functions that can be linked to the interface.

Retinoic acid is necessary for development of the ventral retina in zebrafish.

In the embryonic zebrafish retina, as in other vertebrates, retinoic acid is synthesized from retinaldehyde by two different dehydrogenases, one localized dorsally, the other primarily ventrally. Early in eye development only the ventral enzyme is present. Citral competitively inhibits the ventral enzyme in vitro and decreases the production of retinoic acid in the ventral retina in vivo.