The optimality of the standard genetic code assessed by an eight-objective evolutionary algorithm

Background

The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid replacements in proteins, caused by mutations or translational errors. However, if such optimization in fact occurred, many different properties of amino acids must have been taken into account during the code evolution. Therefore, this problem can be reformulated as a multi-objective optimization task, in which the selection constraints are represented by measures based on various amino acid properties.

Results

To study the optimality of the SGC we applied a multi-objective evolutionary algorithm and we used the representatives of eight clusters, which grouped over 500 indices describing various physicochemical properties of amino acids. Thanks to that we avoided an arbitrary choice of amino acid features as optimization criteria. As a consequence, we were able to conduct a more general study on the properties of the SGC than the ones presented so far in other papers on this topic. We considered two models of the genetic code, one preserving the characteristic codon blocks structure of the SGC and the other without this restriction. The results revealed that the SGC could be significantly improved in terms of error minimization, hereby it is not fully optimized. Its structure differs significantly from the structure of the codes optimized to minimize the costs of amino acid replacements. On the other hand, using newly defined quality measures that placed the SGC in the global space of theoretical genetic codes, we showed that the SGC is definitely closer to the codes that minimize the costs of amino acids replacements than those maximizing them.

Conclusions

The standard genetic code represents most likely only partially optimized systems, which emerged under the influence of many different factors. Our findings can be useful to researchers involved in modifying the genetic code of the living organisms and designing artificial ones.

     

Recent advances in biological production of erythritol

Erythritol is a natural sweetener commonly used in the food and pharmaceutical industries. Produced by microorganisms as an osmoprotectant, it is an ideal sucrose substitute for diabetics or overweight persons due to its almost zero calorie content. Currently, erythritol is produced on an industrial scale through the fermentation of sugars by some yeasts, such as Moniliella sp. However, the popularity of erythritol as a sweetener is still small because of its high retail price. This creates an opportunity for further process improvement. Recent years have brought the rapid development of erythritol biosynthesis methods from the low-cost substrates, and a better understanding of the metabolic pathways leading to erythritol synthesis. The yeast Yarrowia lipolytica emerges as an organism effectively producing erythritol from pure or crude glycerol. Moreover, novel erythritol producing organisms and substrates may be taken into considerations due to metabolic engineering. This review focuses on the modification of erythritol production to use low-cost substrates and metabolic engineering of the microorganisms in order to improve yield and productivity.     

Assessment of the Anticonvulsant Potency of Ursolic Acid in Seizure Threshold Tests in Mice

Ursolic acid (UA) is a plant derived compound which is also a component of the standard human diet. It possesses a wide range of pharmacological properties, i.e., antioxidant, anti-inflammatory, antimicrobial and antitumor, which have been used in folk medicine for centuries. Moreover, influence of UA on central nervous system-related processes, i.e., pain, anxiety and depression, was proved in experimental studies. UA also revealed anticonvulsant properties in animal models of epilepsy and seizures. The aim of the present study was to investigate the influence of UA on seizure thresholds in three acute seizure models in mice, i.e., the 6 Hz-induced psychomotor seizure threshold test, the maximal electroshock threshold (MEST) test and the timed intravenous pentylenetetrazole (iv PTZ) infusion test. We also examined its effect on the muscular strength (assessed in the grip strength test) and motor coordination (estimated in the chimney test) in mice. UA at doses of 50 and 100 mg/kg significantly increased the seizure thresholds in the 6 Hz and MEST tests. The studied compound did not influence the seizure thresholds in the iv PTZ test. Moreover, UA did not affect the motor coordination and muscular strength in mice. UA displays only a weak anticonvulsant potential which is dependent on the used seizure model.     

Comparative in vitro study of caecal microbial activity in brown hares and domestic rabbits which were offered the same diet

The products of the microbial activity in the large intestine are an important source of energy for herbivores. A previous study showed differences in caecal methanogenesis and short-chain fatty acid (SCFA) profiles between brown hares and domestic rabbits. The present study was performed on animals which were offered the same diet to eliminate the impact of diet on the comparative analyses of microbial metabolites. Caecal samples of hares and rabbits were incubated in triplicate, i.e. without any supplementary substrate (control) or with the addition of wheat bran or oat bran. Calculated as percentage of body weight, the stomachs of the rabbits were heavier than those of the hares, but caeca of the hares weighed more than those of the rabbits. The total SCFA concentration in caecal samples was higher in rabbits than in hares, and it increased in both species when the supplementary fermentation substrates were added. In hares, the molar proportion of propionate was higher and that of butyrate was lower compared to rabbits. The addition of substrate decreased acetate and propionate but increased the molar proportion of butyrate. Microbial fermentation resulted in greater gas release in rabbit caecal samples compared to those of hares. Methanogenesis tended to be lower in hares than in rabbits, but high individual variability was observed, especially in hares. Our study stated lower microbial activity in the caeca of brown hares compared to domestic rabbits. The presented results might lead to assumption that differences between fermentation patterns were not caused by diet but resulted from the peculiarities of both species.     

Consortia formed by yeasts and acetic acid bacteria <Emphasis Type="Italic">Asaia</Emphasis> spp. in soft drinks

Yeast strains and acetic acid bacteria were isolated from spoiled soft drinks with characteristic flocs as a visual defect. Polymerase chain reaction and amplification of a partial region of the LSU rRNA gene identified the bacteria as Asaia spp. Sequence analysis of the D1/D2 region of the 26S rDNA in turn identified the yeast isolates as Wickerhamomyces anomalus, Dekkera bruxellensis and Rhodotorula mucilaginosa. The hydrophobicity and adhesion properties of the yeasts were evaluated in various culture media, taking into account the availability of nutrients and the carbon sources. The highest hydrophobicity and best adhesion properties were exhibited by the R. mucilaginosa cells. Our results suggest that Asaia spp. bacterial cells were responsible for the formation of flocs, while the presence of yeast cells may help to strengthen the structure of co-aggregates.     

Multi-locus sequence typing (MLST) of non-fermentative Gram-negative bacilli isolated from bloodstream infections in southern Poland

Non-fermentative Gram-negative bacilli are now one of the most important causes of severe infections in Polish hospitals. Acinetobacter species are serious concern because of the high prevalence of multi-drug resistance among strains. Resistance profiles for 53 Gram-negative non-fermentative blood isolates were done. MLST was carried out using 44 strains representing the most commonly isolated species: A. baumannii, P. aeruginosa, and S. maltophilia. MLST revealed that all 22 A. baumannii belonged to sequence type (ST) 2. The P. aeruginosa isolates belonged to 10 different STs. Four S. maltophilia isolates matched STs present in the database (ST4, ST15, ST116, ST142), seven isolates showing novel sequence types. Among P. aeruginosa and S. maltophilia PFGE confirmed the genetical variety of strains.     

Intra-seasonal variation in zooplankton availability,chick diet and breeding performance of a high Arctic planktivorous seabird

Different phenological responses to climate changes by species representing preys and predators may lead to mismatch between functionally dependent components of an ecosystem, with important effects on its structure and functioning. Here, we investigate within-season variation in zooplankton availability, chick diet composition and breeding performance of a small planktivorous seabird, the little auk (Alle alle) in two large colonies in Hornsund and Magdalenefjorden, Spitsbergen, differing in synchrony of breeding (11-day vs. 22-day hatching period, respectively). Assuming similar zooplankton phenology and existing differences in duration of the little auk breeding period, we expected lower availability of the preferred food in the less synchronized colony in Magdalenefjorden and in consequence a negative effect on nestling body mass and survival. We found that in both colonies Calanus glacialis (copepodite stage CV) was the most important prey item in the chick diet making up 68–87 % of the biomass and energy of all prey items. The only exception was the end of the chick-rearing period in Magdalenefjorden, when contribution of this prey item was significantly lower (24–26 %). Thus, late breeders in Magdalenefjorden were apparently mismatched regarding C. glacialis CV availability. However, the hatching date did not affect birds fitness (reproductive output and chick pre-fledging mass) significantly. Results of our study indicate that little auks breeding on Spitsbergen can respond to a wide range of environmental conditions and prey availabilities through the plasticity of their foraging behaviour, which may help them to maintain their optimum fitness level in changing and unpredictable environments.