In the paper, the problem of isothermic DNA sequencing by hybridization, without any errors in its input data, is presented and an exact polynomial-time algorithm solving the problem is described. The correctness of the algorithm is con.rmed by an enumerative proof.

DNA sequencing remains one of the most important problems in molecular and computational biology. One of the methods used for this purpose is sequencing by hybridization. In this approach usually DNA chips composed of a full library of oligonucleotides of a given length are used, but in principle it is possible to use another types of chips. Isothermic DNA chips, being one of them, when used for sequencing may reduce hybridization error rate. However, it was not clear if a number of errors following from subsequence repetitions is also reduced in this case. In this paper a method for estimating resolving power of isothermic DNA chips is described which allows for a comparison of such chips and the classical ones. The analysis of the resolving power shows that the probability of sequencing errors caused by subsequence repetitions is greater in the case of isothermic chips in comparison to their classical counterparts of a similar cardinality. This result suggests that isothermic chips should be chosen carefully since in some cases they may not give better results than the classical ones.

Field and laboratory protocols that originally led to the success of published studies have previously been only briefly laid out in the methods sections of scientific publications. For the sake of repeatability, we regard the details of the methodology that allowed broad−range DNA studies on deep−sea isopods too valuable to be neglected. Here, a com− prehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep−sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than universal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep−sea isopods with a success rate of 45–79% varying with family. To improve this, we recommend the development of taxon−specific primers.

In recent years, two developments revolutionized the molecular genetics. The first one is an enormously improved technique of the DNA sequencing. It is now possible to obtain in couple of hours and on the low cost, the full sequence of the human genome. The second one is the invention of the CRISPR-Cas technique, which allows the precise manipulations of genomes of living organisms. This technique was already successfully applied to “repair” human genes responsible for hereditary diseases. To some astonishment, applications of genetic engineering to humans does not bring protests of general public, while similar manipulations pf plants genomes are considered an dangerous. In Poland and in some other countries, parliaments introduced an extremely restrictive laws, which in practice makes cultivation of GM plants outside laboratories impossible. This is caused by the ignorance of the general public and by opposition of catholic church which considers genetic modifications of all organisms as contradictory with Gods will. The most common modification of plants is an introduction into their genomes of the single gene from the bacterium Bacillus thuringensis, what make the plant resistant to harmful insects. According to WHO, neither the manipulation mentioned above, nor manipulations of the other kind, do not pose any danger to humans.

Mycoplasma bovis is a highly contagious pathogen that causes clinical or subclinical mastitis. The present study was aimed for the isolation, molecular characterization and antibiogram determination of M. bovis from raw milk samples. Milk samples were collected randomly from lactating cows and buffaloes from different tehsils of district Faisalabad, Pakistan. Samples were inoculated on modified Hayflick medium and biochemical tests were performed for further confirmation of isolated M. bovis. Out of total 400 milk samples, 184 (46%) samples were found positive for culture method. The 16S-rRNA gene polymerase chain reaction was performed for molecular characterization of isolated M. bovis strains. Out of total 400 milk samples, 240 (60%) positive for M. bovis through PCR method were examined. The 16S-rRNA gene PCR positive isolated M. bovis strains were sequenced and results were compared using Maximum-likelihood method and sequenced strains of M. bovis were aligned and analyzed by Clustal W software. Antibiogram of isolated M. bovis strains was analyzed by disc diffusion assay against eight commonly used antibiotics. Tylosin (30μg) and Tilmicosin (15ug) showed inhibition zones of 32.34 ± 1.10 mm and 17.12 ± 0.93 mm respectively against isolated M. bovis which were found sensitive. Isolated M. bovis was found resistant to other commonly used antibiotics. Statistical analysis revealed that p-value was < 0.05 and the odds ratio was >1.0 at 95% CI. This study complemented the lack of epidemiological knowledge of molecular characterization, comparative effectiveness and resistance trends of isolated M. bovis strains against commonly used antibiotics.