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.

Salmonellosis is a public health concern worldwide and also causes huge losses to the piggery industry. A total of 457 fecal samples were collected from organized and unorganized farms including indigenous and crossbreed piglets of North East India. Salmonella isolates were serotyped, screened for their virulence genes, characterized for drug resistance pattern and representative isolates were cloned and sequenced for their partial length enterotoxin (stn) gene. A total of 8.31% Salmonella were identified with higher prevalence observed in unorganized compared to organized farms and higher detection level in cross breed compared to indigenous piglets. Salmonella typhimurium (65.78%) was found to be the predominant serovar and irrespective of serovars high number of isolates (68.4%) harboured enterotoxin gene. The isolates were multidrug resistant showing highest resistance against cefalexin (77.31%). Sequence analysis of stn gene showed two isolates having diverse sequence compared to other isolates. Our study revealed the significance of Salmonella as important pathogen with zoonotic potential between porcine and human populations. This is probably the first systematic study of Salmonella species associated with piglet diarrhea in India.

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.

Anaerobic digestion is an important technology for the bio-based economy. The stability of the process is crucial for its successful implementation and depends on the structure and functional stability of the microbial community. In this study, the total microbial community was analyzed during mesophilic fermentation of sewage sludge in full-scale digesters.

The digesters operated at 34–35°C, and a mixture of primary and excess sludge at a ratio of 2:1 was added to the digesters at 550 m3/d, for a sludge load of 0.054 m3/(m3·d). The amount and composition of biogas were determined. The microbial structure of the biomass from the digesters was investigated with use of next-generation sequencing.

The percentage of methanogens in the biomass reached 21%, resulting in high quality biogas (over 61% methane content). The abundance of syntrophic bacteria was 4.47%, and stable methane production occurred at a Methanomicrobia to Synergistia ratio of 4.6:1.0. The two most numerous genera of methanogens (about 11% total) were Methanosaeta and Methanolinea, indicating that, at the low substrate loading in the digester, the acetoclastic and hydrogenotrophic paths of methane production were equally important. The high abundance of the order Bacteroidetes, including the class Cytophagia (11.6% of all sequences), indicated the high potential of the biomass for efficient degradation of lignocellulitic substances, and for degradation of protein and amino acids to acetate and ammonia.

This study sheds light on the ecology of microbial groups that are involved in mesophilic fermentation in mature, stably-performing microbiota in full-scale reactors fed with sewage sludge under low substrate loading.

Species of the genus Salsola belong to the family Chenopodiaceae and are associated with large saline areas in eastern Iran. The aim of the study was to isolate and characterize the endophytic and phytopathogenic fungal communities from non-mycotrophic Salsola species. Sampling was done from different parts of Salsola plants in the Birjand region in 2017 and 2018. Isolation and identification of fungal isolates were done using biological characteristics and ITS region sequences. The pathogenicity of the representative isolates was investigated by cultivating disinfected Salsola incanescens seeds under greenhouse conditions and inoculating seedlings with a fungal spore suspension from 7 day old fungal colonies on PDA media. Based on morphological and molecular data, 27 isolates from 11 fungal species were isolated and identified from Salsola tissues. Alternaria alternata, A. chlamydospora, Aspergillus terreus, Macrophomina phaseolina, Fusarium longipes, Ulocladium atrum, and Talaromyes pinophilus caused root or stem rotting and yellowing leaf of S. incanescens under greenhouse conditions. Aspergillus niger induced S. incanescens crown swelling without any pathogenicity. Clonostachys rosea, F. redolens and F. proliferatum grew as endophytic fungi on S. incanescens roots. This is the first report of phytopathogenic M. phaseolina, F. longipes, T. pinophilus, endophytic F. redolens and A. niger as a swelling agent on S. incanescens.

Staphylococcus pseudintermedius (SP) and methicillin-resistant SP (MRSP) is one of the most important veterinary pathogens in the dog. Herein, from a total of 126 S. pseudintermedius strains, 23 MRSP (18%) were identified. Multi-Locus Sequence Typing (MLST) revealed that most of MRSP strains belonged to ST71 (26%), which have been already reported in Italy and other countries. Interestingly, nine new sequence types (39%), from 1053 up to 1061, were described for the first time. Moreover, the isolated MRSP strains showed relevant antibiotic resistance profiles. This report highlights the circulation of new sequence types of MRSP in Italy and underlines the need of a global epidemiological surveillance to limit the increasing spread of multidrug-resistant MRSP strains worldwide, since they may represent a considerable concern for dog’s health.

In 1985–2002 thirteen weeds resistant to atrazine were selected by a repeated application of triazine herbicides on arable land, in orchards, non-agricultural land and at railways in the Czech Republic. Recently Digitaria sanguinalis biotypes resistant to atrazine have been found at three railway junctions. Long-lasting application of the active ingredient imazapyr at railways caused selection of resistant Kochia scoparia biotypes. High resistance to chlorsulfuron has been discovered in five Apera spica-venti biotypes originating in winter cereals fields. The molecular basis of resistance to atrazine has been identified in the following weeds: Kochia scoparia, Solanum nigrum, Senecio vulgaris, Conyza canadensis, Digitaria sanguinalis, Amaranthus retroflexus and Chenopodium album. The resistance was conferred by a glycine for serine substitution at residue 264 of the D1 protein in all of those weeds. The resistance to imazapyr in Czech Kochia scoparia biotypes was conferred by a mutation at codon 574 of the ALS gene. Analysis of the results of DNA sequencing indicated, that the mutation induced a leucine for tryptophane substitution. There was excellent correspondence between the phenotypic resistance to herbicides of individual plants and the presence of mutations.

The paper presents a Car Sequencing Problem, widely considered in the literature. The issue considered by the researchers is only a reduced problem in comparison with the problem in real automotive production. Consequently, a newconcept, called Paint Shop 4.0., is considered from the viewpoint of a sequencing problem. The paper is a part of the previously conducted research, identified as Car Sequencing Problem with Buffers (CSPwB), which extended the original problem to a problem in a production line equipped with buffers. The new innovative approach is based on the ideas of Industry 4.0 and the buffer management system. In the paper, sequencing algorithms that have been developed so far are discussed. The original Follow-up Sequencing Algorithm is presented, which is still developed by the authors. The main goal of the research is to find the most effective algorithm in terms of minimization of painting gun changeovers and synchronization necessary color changes with periodic gun cleanings. Carried out research shows that the most advanced algorithm proposed by the authors outperforms other tested methods, so it is promising to be used in the automotive industry.

In Polish coal mining, medium voltage power distribution networks operate with an insulated neutral point. Zero-sequence current transformers are the basic sensors that generate input signals for earth-fault protection relays. In the literature, the problem of frequency response analysis of various types of current transformers has been examined many times, e.g. [1] [2], but not for zero-sequence current transformers so far. As part of the work, two types of zero-sequence current transformers in the range from 0.1 Hz to 100 kHz were tested. Both the change of the current ratio and the angular shift between the transformer secondary current and the total primary current were analyzed.

Bacteria from the Simkaniaceae family are intracellular parasites belonging to the Chlamydiales order, detected in surface waters, drinking water, chlorine water, and in wastewater. Its main representative, Simkania negevensis, is pathogenic to humans and animals, especially fishes, as it principally causes respiratory tract diseases. Bacteria from this family are also capable of surviving and existing in free-living amoebas, omnipresent in the natural environment, which makes them an additional risk for human and animal health. The aim of the present study was to search for representatives of this family in freshwaters from the Odra River and two municipal lakes (Rusałka and Goplana). Out of 100 water samples analysed, the sequence of bacteria of Simkaniaceae family was found just in 1 percent, because phylogenetic analysis revealed that the obtained OdraWCh30 sequence shows 93% similarity to Simkania negevensis strain Z as well as 87% similarity to Candidatus Syngnamydia salmonis isolate Ho-2008 and Candidatus Syngnamydia salmonis isolate VS10102006 and 84-85% similarity to endosymbiont of Xenoturbella westbladi, Simkaniaceae bacterium clone SM081012-5s and Candidatus Syngnamydia venezia strain Pi3-2. This is the first case of detecting sequence of bacteria of Simkaniaceae family in the aquatic environment in Poland.

The welfare and healthy growth of poultry under intensive feeding conditions are closely related to their living environment. In spring, the air quality considerably decreases due to reduced ventilation and aeration in cage systems, which influences the meat quality and health of broilers during normal growth stages. In this study, we analyzed the airborne bacterial communities in PM2.5 and PM10 in cage broiler houses at different broiler growth stages under intensive rearing conditions based on the high-throughput 16S rDNA sequencing technique. Our results revealed that PM2.5, PM10 and airborne microbes gradually increased during the broiler growth cycle in poultry houses. Some potential or opportunistic pathogens, including Acinetobacter, Pseudomonas, Enterococcus, Microbacterium, etc., were found in the broiler houses at different growth stages. Our study evaluated variations in the microbial communities in PM2.5 and PM10 and potential opportunistic pathogens during the growth cycle of broilers in poultry houses in the spring. Our findings may provide a basis for developing technologies for air quality control in caged poultry houses.

This paper presents a multidisciplinary model built across linguistics and selected research and hypotheses in the field of quantum physics and molecular biology. The conceptual link between the biological concept of protein sequencing and the anthropocentric assumptions concerning the operationalization of language rules will be discussed. The multidisciplinary model shows the link between the concept of sequencing language rules and constructing textemes.

The paper presents the issue of container handling processes at a railroad intermodal terminal. The main purpose of this paper is the assessment of the handling equipment utilization and the associated energy consumption. The authors analyze how the road vehicle availability at the moment specified in the containers loading schedule influences the total handling equipment operation time as well as the necessary number of handling equipment. It is assumed that vehicles planned for loading of import containers may be late for loading, which causes some interruptions in the loading schedule. Such interruptions are identified with the necessity to handle the next container for which the road vehicle is already waiting, which influences the handling equipment utilization and, finally, energy consumption. The general mathematical model of the problem developed in the FlexSim simulation software was presented. Based on the simulation research, it pointed out that proper road vehicles loading sequencing can significantly reduce handling equipment operation time, and thus energy consumption, costs, and CO₂ emissions. The literature analysis presented in the paper indicates that most of the research in the field of intermodal transport is focused on operations optimization in container ports. There are differences between two types of intermodal terminals in operation procedures and rules. That is why the authors decided to undertake the problem of road vehicle sequencing including their random availability and its influence on handling device operation time, which has not been considered in the literature so far.