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Number of results: 9
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Abstract

The aim of the paper was to study the epizootic situation of babesiosis in the cattle population in eastern Poland and possibly to determine what species of protozoa infects Polish cattle. Blood samples for molecular analysis (real time PCR) were collected from 192 dairy cows from various farms located in eastern Poland. The infection was detected in 10.4% of the samples. All animals were infected with Babesia occultans which sequence of the 18S RNA gene fragment showed a 93.1%, homology with the sequence of B. occultans EU 376017. This is the first report about the detection of B. occultans DNA in asymptomatic cattle in eastern Poland.
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Abstract

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.
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Abstract

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.
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Abstract

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.
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Abstract

The lithostratigraphy, biostratigraphy, sequence stratigraphy, ammonite and inoceramid faunas of the Upper Albian, Cenomanian, and Lower Turonian Karai Formation, the highest unit of the Uttatur Group in the Pondicherry Sub-Basin of the Cauvery Basin in Tamil Nadu, south India, are documented. Detailed logs and descriptions of sections between Karai and Kulakkalnattam, Odiyam and Kunnam, and north-west of Garudamangalam are presented. They provide the evidence for an ammonite zonal scheme that can be correlated in detail with sequences developed in Europe, with successive Upper Albian zones of Pervinquieria (Subschloenbachia) rostrata and P. (S.) perinflata (the latter on slight evidence), Cenomanian zones of Mantelliceras mantelli, Cunningtoniceras cunningtoni, Calycoceras (Newboldiceras) asiaticum, Pseudo calycoceras harpax, Euomphaloceras septemseriatum and Pseudspidoceras footeanum. The Lower Turonian is represented by a Neoptychites cephalotus–Mytiloides borkari fauna. Over 120 ammonite species are described, of which Puzosia (Bhimaites) falx, Protacanthoceras parva, Watinoceras elegans, Euomphaloceras varicostatum, Kamerunoceras multinodosum, and Carthaginites multituberculatus are new. The new genus Kunnamiceras, with Ammonites tropicus Kossmat, 1865 as type species, is interpreted as a paedomorphic dwarf derivative of Pseudocalycoceras harpax (Stoliczka, 1864). Ammonite faunas from shales are dominated by feebly-ornamented taxa: leiostraca; those from sandstones by strongly ornamented taxa: trachyostraca, differences interpreted as reflecting the preferred habits of adults in life. 15 species of inoceramid bivalves, including a newly described species Inoceramus chiplonkari, are recognised, with a mixed East African–Euramerican–North Pacific affinity. On the basis of the stratigraphic framework developed, a sequence stratigraphic interpretation of the Karai Formation is proposed, and correlated with those recognised in Europe, Morocco, and the United States Gulf Coast and Western Interior.
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Abstract

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.
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Abstract

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.
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Abstract

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.
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Abstract

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.
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