Ubiquitin carboxyl-terminal peptides. Substrates for ubiquitin activating enzyme

The carboxyl terminus of ubiquitin is activated in the presence of ATP to enter the ubiquitin cycle in cells. Peptides corresponding to the COOH-terminal region of ubiquitin were synthesized to investigate their effects on the ATP/ubiquitin-dependent proteolytic pathway. Their activities in the PPi exchange assay with ubiquitin activating enzyme (E1) were proportional to their length. The hexapeptide Ac-Leu-Arg-Leu-Arg-Gly-Gly reacted with ATP to form an enzyme-adenylate-hexapeptide complex and at high concentrations was 20-25% as active as human ubiquitin in the PPi exchange assay with E1. However, the hexapeptide was not transferred to the sulfhydryl "thiol" site on E1. In addition, the COOH-terminal peptides did not support the degradation of 125I-bovine serum albumin in the reticulocyte lysate system. A nonhomologous peptide of equivalent length was inactive in all assays. Thus, synthetic COOH-terminal peptide(s) of ubiquitin can partially substitute for ubiquitin in its reactions with E1 but do not support subsequent steps of the energy-dependent proteolytic pathway. These results show that it may be possible to design small molecules that either serve as substrates or inhibitors for other specific steps in ubiquitin-dependent pathways.     

lin-17 mutations of Caenorhabditis elegans disrupt certain asymmetric cell divisions

The identification of a gene necessary for the asymmetry of cell division would be an important first step toward understanding how sister cells come to differ in their developmental fates. The lin-17 gene of the nematode Caenorhabditis elegans is an excellent candidate for being such a gene. lin-17 mutations cause several blast cells that normally generate sister cells of two distinct types to generate instead sister cells of the same type. Moreover, lin-17 mutations cause sister cells to be equal in size as well as equivalent in developmental fate, suggesting that lin-17 acts at or prior to the asymmetric cell division. The lin-17 gene product is involved in asymmetric cell divisions in a variety of tissues, indicating that lin-17 functions in a general mechanism for the establishment of cellular asymmetry in parent cells.     

ONYCHOMYCOSIS OF THE FEET—Treatment with Griseofulvin

Griseofulvin, a new orally administered antifungal antibiotic which has proved to be effective for the treatment of a wide variety of superficial fungus infections of man, was used in the treatment of 51 patients with infections of the toenails due to T. rubrum. Thirty-four of the patients were treated with griseofulvin alone and seven were treated with griseofulvin combined with surgical avulsion of all involved toenails. The remaining ten had bilateral infections, and avulsion was done on one foot but not the other before griseofulvin therapy was begun.Of 34 patients who were treated with griseofulvin alone, few had complete cure even after prolonged treatment. Some nails showed improvement for a time, then no further gain; some showed no improvement; some showed resistant wedges of infection which penetrated proximally toward the posterior nail fold.In the instances of surgical avulsion, clinically normal nails regrew during griseofulvin therapy. This simple procedure, with thorough removal of all underlying keratinous debris, apparently did away with foci of possible reinfection.The results of the study indicated that surgical avulsion of the toenails in combination with griseofulvin therapy is an effective and practical method of treating onychomycosis of the toenails due to T. rubrum.     

Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks.

The applications of artificial neural networks to the prediction of structural and functional features of protein and nucleic acid sequences are reviewed. A brief introduction to neural networks is given, including a discussion of learning algorithms and sequence encoding. The protein applications mostly involve the prediction of secondary and tertiary structure from sequence. The problems in nucleic acid analysis tackled by neural networks are the prediction of translation initiation sites in Escherichia coli, the recognition of splice junctions in human mRNA, and the prediction of promoter sites in E. coli. The performance of the approach is compared with other current statistical methods.     

Plant community dynamics in a calcareous grassland under climate change manipulations

This study investigates the effects of field manipulations of local climate to determine the potential impact of climate change on plant community dynamics in a calcareous grassland. The experimental site is located in a grassland at the Wytham estate, Oxfordshire, UK. The one hectare study area is within a 10 ha abandoned arable field on Jurassic corallian limestone. Two climate change scenarios were used: warmer winters with increased summer rainfall and warmer winters with summer drought. Plant cover and species richness were significantly increased in plots receiving supplemented summer rainfall, while the amount of litter was significantly reduced. Litter formation was significantly increased by winter warming and drought. The responses of the plant community to the climate manipulations were related to the life-history attributes of the dominant species. Seedling recruitment was limited by microsite availability, which also varied in the different climate manipulations. The results are discussed in terms of successional dynamics. They suggest that warmer winters may delay succession, as gap formation in the sward will provide sites for colonisation of annuals, thereby enabling their persistence in the sward. Under wetter conditions during summer, perennial grasses tend to close the sward, thereby inhibiting the establishment of later successional species.     

Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA

Transposable and interspersed repetitive elements (TIREs) are ubiquitous features of both prokaryotic and eukaryotic genomes. However, controversy has arisen as to whether these sequences represent useless selfish DNA elements, with no cellular function, as opposed to useful genetic units.In this review, we selected two insect species, the Dipteran Drosophila and the Lepidopteran Bombyx mori (the silkmoth), in an attempt to resolve this debate. These two species were selected on the basis of the special interest that our laboratory has had over the years in Bombyx with its well known molecular and developmental biology, and the wealth of genetic data that exist for Drosophila. In addition, these two species represent contrasting repetitive element types and patterns of distribution. On one hand, Bombyx exhibits the short interspersion pattern in which Alu-like TIREs predominate while Drosophila possesses the long interspersion pattern in which retroviral-like TIREs are prevalent. In Bombyx, the main TIRE family is Bm-1 while the Drosophila group contains predominantly copia-like elements, non-LTR retroposons, bacterial-type retroposons and fold-back transposable elements sequences. our analysis of the information revealed highly non-random patterns of both TIRE biology and evolution, more indicative of these sequences acting as genomic symbionts under cellular regulation rather than useless or selfish junk DNA. In addition, we extended our analysis of potential TIRE functionality to what is known from other eukaryotic systems. From this study, it became apparent that these DNA elements may have originated as innocuous or selfish sequences and then adopted functions. The mechanism for this conversion from non-functionality to specific roles is a process of Coevolution between the repetitive element and other cellular DNA often times in close physical proximity. The resulting interdependence between repetitive elements and other cellular sequences restrict the number of evolutionarily successful mutational changes for a given fuction or cistron. This mutual limitation is what we call genome canalization. Well documented examples are discussed to support this hypothesis and a mechanistic model is presented for how such genomic canalization can occur. Also proposed are empirical studies which would support or invalidate aspects of this hypothesis.     

On the conformation of proteins: The handedness of the β-strand-α-helix-β-strand unit

The β-strand-α-helix-β-strand unit consists of two parallel, but not necessarily adjacent, β-strands which lie in a β-pleated sheet and are connected by one or more α-helices. This unit, which occurs in 17 functionally different globular proteins, may adopt a right- or a left-handed conformation. An analysis of the distribution shows that 57 out of the 58 units are right-handed. If the unit had no right-handed preference, the probability of observing such a distribution by chance is 10^?16. This may be explained in terms of the twist of the β-sheet which is shown to favour a right-handed unit, as otherwise steric hindrance occurs in the loop regions. We show that the right-handed strand-helix-strand unit determines the sense of the super-secondary structure found in the dehydrogenases and of related folds found in other structures. The evolutionary relationships between proteins containing this unit are re-evaluated in terms of this preference. The high probability that the unit will fold with a right-handed conformation has implications for the prediction of tertiary structure.     

Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys

Using the strictly neutral model as a null hypothesis, we tested for deviations from expected levels of nucleotide polymorphism at the alcohol dehydrogenase locus (Adh-1) within and among four species of pocket gophers (Geomys bursarius major, G. knoxjonesi, G. texensis llanensis, and G. attwateri). The complete protein-encoding region was examined, and 10 unique alleles, representing both electromorphic and cryptic alleles, were used to test hypotheses (e.g., the neutral model) concerning the maintenance of genetic variation. Nineteen variable sites were identified among the 10 alleles examined, including 9 segregating sites occurring in synonymous positions and 10 that were nonsynonymous. Several statistical methods, including those that test for within-species variation as well as those that examine variation within and among species, failed to reject the null hypothesis that variation (both within and between species of Geomys) at the Adh locus is consistent with the neutral theory. However, there was significant heterogeneity in the ratio of polymorphism to divergence across the gene, with polymorphisms clustered in the first half of the coding region and fixed differences clustered in the second half of the gene. Two alternative hypotheses are discussed as possible explanations for this heterogeneity: an old balanced polymorphism in the first half of the gene or a recent selective sweep in the second half of the gene.