PDBsum extras: SARS‐CoV‐2 and AlphaFold models

The PDBsum web server provides structural analyses of the entries in the Protein Data Bank (PDB). Two recent additions are described here. The first is the detailed analysis of the SARS‐CoV‐2 virus protein structures in the PDB. These include the variants of concern, which are shown both on the sequences and 3D structures of the proteins. The second addition is the inclusion of the available AlphaFold models for human proteins. The pages allow a search of the protein against existing structures in the PDB via the Sequence Annotated by Structure (SAS) server, so one can easily compare the predicted model against experimentally determined structures. The server is freely accessible to all at http://www.ebi.ac.uk/pdbsum.     

Cryoconservation—archiving for the future

Mouse genetics is set to play a pivotal role in the key post-genome challenge—the study of mammalian gene function. Addressing this challenge will involve the development and application of systematic mutagenesis approaches. The expanding mouse mutant resource that will result threatens to overwhelm the currently available animal facility space. Cryopreservation of both mouse embryos and spermatozoa is currently widely employed for the efficient archiving of mouse stocks. Distribution and dissemination of new and existing mouse strains is simplified by the availability of extensive frozen archives. Also, the availability of archives of frozen spermatozoa provides a potential powerful route for the production of backcross progeny for rapid genetic mapping. Moreover, frozen oocytes and ovaries may offer a valuable addition to the current cryopreservation approaches. Comprehensive mouse mutant archives will provide an essential resource for mammalian genetics throughout the 21^st century. Received: 16 December 1999 / Accepted: 17 December 1999     

Low luteinizing hormone enhances spatial memory and has protective effects on memory loss in rats

Though several studies have suggested that estradiol improves hippocampal-dependent spatial memory, the effects of other hormones in the hypothalamic–pituitary–gonadal axis on memory have largely been ignored. Estradiol and luteinizing hormone (LH) are generally inversely related and LH may significantly affect spatial memory. Ovariectomized (ovx) rats treated with Antide (a gonadotropin releasing hormone receptor antagonist) had low LH levels and showed enhanced spatial memory, comparable to treatment with estradiol. Antide-treated ovx females retained spatial memory longer than estradiol-treated ovx females. Deficits in spatial memory are a primary symptom of neurodegenerative disorders including Alzheimer's disease (AD). Treatment with Antide prevented spatial memory deficits in a neurotoxin-induced model typical of early AD. These data suggest that memory impairments seen in female rats after ovariectomy or women after menopause may be due to high LH levels and that a reduction in LH enhances memory. These results also implicate an LH lowering agent as a potential preventative therapy for AD.     

The promotive effect of combustion products from plant vegetation on the release of seeds from dormancy

In darkness, dormancy was imposed on seeds of lettuce (Lactuca sativa L. cv. Grand rapids) by high temperature and on seeds of oilseed rape (Brassica napus L. cv. Apex) by osmotic stress using polyethylene glycol (PEG 8000). In both cases, dormancy was broken by incubating the seeds in aqueous extracts of combustion products from Salix viminalis wood chips or Themeda triandra leaves. Dormancy of rapeseed, but not lettuce, was also broken by a solution of smoke from burnt straw of Triticum aestivum. The greatest stimulation from burnt vegetation was achieved with an aqueous extract of pyrolysed willow wood chips, which had been subjected to temperatures of up to 800 °C during combustion in a down-draught gasifier. This suggests that some biologically active substances obtained from combustion of plant tissues are highly heat-stable.     

Cytotoxicity of N6-cycloalkylated adenine and adenosine analogs to mouse hepatoma cells

Cytotoxic effect(s) of N6-cycloalkylated adenine and adenosine derivatives, upon the viability of mouse hepatoma cells, were studied in vitro. N6-Cyclopropyl- and N6-cyclobutyladenine and adenosine derivatives (33 micrograms/ml; 24-48 h) exerted significant cytotoxic effects upon the cells. N6-Cyclopentyl- and N6-cyclohexyladenines exerted similar effects under different experimental conditions (133-166 micrograms/ml; 48-72 h), while no significant cytotoxic effect(s) were observed with the corresponding adenosine derivatives under these conditions. Observed physical changes in the treated cells included cell elongation, short stubby filaments, wide intracellular spaces and ruptured cell membranes. N6-Cycloalkylated nucleosides were usually more cytotoxic than the cycloalkylated bases.     

Protein motifs and data-base searching

Protein structure and sequence motifs are now recognized for many different protein families and topologies. To aid identification and use of these motifs in modelling and prediction, it has become necessary to establish consistent data bases of protein structure, including not only coordinates, but also derived data such as secondary structure location and solvent accessibilities. This article describes first attempts to construct such data bases and explains how they can be used.     

Natural selection promotes divergence of transferrin among salmonid species

Transferrin is an iron-binding protein that plays an important role in iron metabolism and resistance to bacterial infection in a variety of organisms. A comparison of transferrin coding sequences from four salmonid species shows that the rate of evolution at nonsynonymous sites is significantly higher than the rate at synonymous sites, suggesting that positive natural selection for new alleles has played an important role in the evolution of transferrin in some salmon species. We hypothesize that the selective agent driving rapid divergence is interactions between host transferrin and the iron-scavenging proteins of pathogenic bacteria.