Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans

Recently, we have defined and analyzed over 1800 orthologous human and rodent genes. Here we extend this work to compare human and Caenorhabditis elegans coding sequences. 1880 human proteins were compared with about 20000 predicted nematode proteins presumably comprising nearly the complete proteome of C. elegans. We found that 44% of human/rodent orthologs have convincing nematode counterparts. On average, the amino acid similarity and identity between aligned human and C. elegans orthologous gene products are 69.3% and 49.1% respectively, and the nucleotide identity is 49.8%. Detailed investigation of our results suggests that some nematode gene predictions are incorrect, leading to erroneous pairing with human genes (e.g. calcineurin and polymerase II elongation factor III). Furthermore, other proteins (i.e. homologs of human ribosomal proteins S20 and L41, thymosin) are missing entirely from the nematode proteome, suggesting that it may not be complete. These results underscore the fact that metazoan gene prediction is a very challenging task and that most computer-predicted nematode genes require supporting evidence of their existence from comparative genomics and/or laboratory investigation.     

Mastering seeds for genomic size nucleotide BLAST searches

One of the most common activities in bioinformatics is the search for similar sequences. These searches are usually carried out with the help of programs from the NCBI BLAST family. As the majority of searches are routinely performed with default parameters, a question that should be addressed is how reliable the results obtained using the default parameter values are, i.e. what fraction of potential matches have been retrieved by these searches. Our primary focus is on the initial hit parameter, also known as the seed or word, used by the NCBI BLASTn, MegaBLAST and other similar programs in searches for similar nucleotide sequences. We show that the use of default values for the initial hit parameter can have a big negative impact on the proportion of potentially similar sequences that are retrieved. We also show how the hit probability of different seeds varies with the minimum length and similarity of sequences desired to be retrieved and describe methods that help in determining appropriate seeds. The experimental results described in this paper illustrate situations in which these methods are most applicable and also show the relationship between the various BLAST parameters.     

Induction and stimulation of in vitro flowering of Pharbitis nil by cytokinin and gibberellin

The influence of BA, GA₃ and IAA applied successively onflower bud formation in shoot apices of Pharbitis nil hasbeen investigated. The shoot apices were isolated from seedlings cultivatedunder non-inductive continuous light and from seedlings exposed to asubinductive (12 h) dark period. BA and GA₃ introducedsuccessively into culture medium replaced the inductive night, causing theflowering of plantlets in completely non-inductive continuous light (optimalconcentration of BA – 10^–7–10^–6mol dm^–3, GA₃ –10^–7–10^–6 moldm^–3) and stimulated this process under thesubthresholdinduction. These hormones applied in reverse sequence (in the first placeGA₃, then BA) did not affect flowering of explants. IAA nullifiedthestimulating effect of BA and GA₃. The influence of phytohormones onflowering may result from the change of growth correlations within the shootapical meristem.     

Quantitative determination of creatine kinase release from herring (Clupea harengus) spermatozoa induced by tributyltin

Creatine kinase (CK, ATP creatine phosphotransferase, EC 2.7.3.2) is an enzyme participating in ATP regeneration, which is the primary source of energy in living organisms. We demonstrated that CK from herring spermatozoa has high activity ( approximately 452 micromol/min/g of fresh semen) and has a different electrophoretic mobility from isoenzymes present in skeletal muscle. In our study, we investigated toxic effect of tributyltin (TBT) on herring spermatozoa using a specific sperm viability kit to observe live and dead sperm cells with a confocal microscope. Treatment of herring spermatozoa with TBT caused a time-dependent decrease of viability: 35% nonviable cells with 5 microM TBT and more than 90% nonviable cells with 10 microM TBT after 6 h exposure. We also monitored CK release from damaged spermatozoa into surrounding medium containing different concentrations of TBT. The higher concentration of TBT was used the more CK release from spermatozoa was observed. We suggest that CK could be a good biomarker of sperm cell membranes degradation in the case when lactate dehydrogenase release from permeabilized cells is not possible for rapid determination of the effect of TBT.     

Molecular models in nickel carcinogenesis

Nickel compounds are known human carcinogens, but the exact molecular mechanisms of nickel carcinogenesis are not known. Due to their abundance, histones are likely targets for Ni(II) ions among nuclear macromolecules. This paper reviews our recent studies of peptide and protein models of Ni(II) binding to histones. The results allowed us to propose several mechanisms of Ni(II)-inflicted damage, including nucleobase oxidation and sequence-specific histone hydrolysis. Quantitative estimations of Ni(II) speciation, based on these studies, support the likelihood of Ni(II) binding to histones in vivo, and the protective role of high levels of glutathione. These calculations indicate the importance of histidine in the intracellular Ni(II) speciation.     

The influence of Bipolaris sorokiniana and Drechslera dictyoides metabolites on cell membrane permeability of Festuca pratensis callus

The aim of this study was the evaluation of membrane permeability of callus cells of several Polish meadow fescue cultivars, which were treated with toxins of two leaf spot pathogens Bipolaris sorokiniana and Drechslera dictyoides. Fungus metabolites were obtained by the method described by Lepoivre et al. (1986). Calli of cultivars ‘Skrzeszowicka’, ‘Skawa’, ‘Westa’, POB 282, POB 383, KOA 186 have been selected on medium with metabolites for two weeks. Next the conductivity test of electrolyte leakage and of total ion contents in the examined tissue was done. On the base of this data the membrane permeability coefficients for each cultivar were calculated. Toxins of B. sorokiniana damaged the cell membranes more strongly than metabolites of D. dictyoides. The significant differences of several objects sensitivity to the influence of B. sorokiniana metabolites were stated. These differences were not observed in the case of the influence of D. dictyoides metabolites on the examined tissue.     

The role of calcium ions in freezing injuries of winter oilseed rape leaves. Effects of calcium channel blockers and mimesis by calcium ionophore

Calcium ionophore A23187 allowing for a calcium ion influx from an apoplast to a cytoplasm, mimicked symptoms of the frost-induced injuries in winter oilseed rape leaves, as estimated by the conductivity method. Both calcium ionophore and freezing treatment induced degradation of phosphatidylcholine. On the other hand lanthanum and gadolinum ions as well as verapamil, the inhibitors of calcium ion channels, decreased the degree of the frost-induced injuries. Lanthanum ions prevented the frost-induced degradation of PC. It is proposed that freezing alters the functioning of calcium ion channels which results in calcium ion influx into a cytosol. This in turn may lead to a degradation of cell membranes.     

Effect of Brood Age on Nestling Diet and Prey Composition in a Hedgerow Specialist Bird,the Barred Warbler Sylvia nisoria

The composition and quality of food provided to nestling birds influence their growth and development and offers key insight into the ecological requirements of birds. One bird species whose feeding ecology is poorly understood is the Barred Warbler (Sylvia nisoria), which utilizes semi-natural shrubby vegetation in agroecosystems. Because Barred Warbler nestlings vary greatly in body mass we hypothesised that diet and prey properties (size, diversity, taxonomic composition, and chitin content and resulting body hardness and digestibility) would differ as the nestlings aged. We quantified the diet based on faecal analysis, sampling faecal sacs from the nestlings pooled into three age classes: 2-3 days old, 4-6 d old, and 7-9 d old. Nestlings were provided a wide diversity of food and a strong relationship existed between food characteristics and nestling age. The youngest nestlings (2-3 d old) had the lowest values of each dietary characteristic (diversity, number and total biomass of prey, and individual prey weight), that were significantly lower than the oldest nestlings (7-9 d old). Nestlings aged 4-6 d exhibited intermediate dietary characteristics. Differences in dietary composition of the six major food types showed marked differences between the individual broods and age categories. Percentages of the number and biomass of soft-bodied prey were highest in the diet of 2-3 d and 4-6 d old nestlings, and decreased with increasing age, whereas the opposite trend was observed in the percentage of intermediately and heavily chitinised prey. Parent Barred Warblers probably preferentially select soft-bodied prey for the youngest nestlings, and satisfy the greater energy demands of the older ones by providing them with a greater variety of prey containing more chitin, as well as plant food. The provisioning of less-readily digestible prey to older nestlings suggests that as the quality of food decreases the quantity increases, implying that the youngest nestlings may be physiologically limited as regards their ability to digest more heavily chitinised prey.