Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping

Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g. local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also noncoding regions are examined

First Complete Genome of the Thermophilic Polyhydroxyalkanoates Producing Bacterium Schlegelella thermodepolymerans DSM 15344

Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates (PHA) – biodegradable polymers representing an alternative to conventional plastics. Here, we present the first complete genome of the type strain S. thermodepolymerans DSM 15344 that was assembled by hybrid approach using both, long (Oxford Nanopore) and short (Illumina) reads. The genome consists of a single 3,858,501bp long circular chromosome with GC content of 70.3%. Genome annotation identified 3,650 genes in total while 3,598 open reading frames belonged to protein coding genes. Functional annotation of the genome and division of genes into clusters of orthologous groups (COG) revealed a relatively high number of 1,013 genes with unknown function or unknown COG, which reflects the fact that only a little is known about thermophilic PHA producing bacteria on a genome level. On the other hand, 270 genes involved in energy conversion and production were detected. This group covers genes involved in catabolic processes which suggests capability of S. thermodepolymerans DSM 15344 to utilize and biotechnologically convert various substrates such as lignocellulose-based saccharides, glycerol, or lipids. Based on the knowledge of its genome, it can be stated that S. thermodepolymerans DSM 15344 is a very interesting, metabolically versatile bacterium with great biotechnological potential

The brand perception of Fairtrade at the Faculty of Economics, University of South Bohemia

The main objective of this bachelor thesis is to analyse how people at the Faculty of Economics perceive the Fairtrade brand. It means, how deep is their knowledge of this brand, what products consumers buy most, why they buy them and how they are satisfied with the quality and price of these products. The work is divided into two patrs: theoretical and practical. The theoretical part is mainly focused on basic information for understanding the essence of the bachelor thesis. The practical part is based on a questionnaire survey between people at the Faculty of Economics. The work concludes with suggestions which improve the current situation of the Fairtrade brand perception at the Faculty of Economics at the University of South Bohemia

Packaging-Free (Zero-Waste) Shops in terms of the Czech market

The main aim of this diploma thesis is to analyse packaging free (zero waste) shops in the conditions of the Czech market from the point of view of consumers and selected zero waste stores. The thesis is divided into two parts: theoretical and practical. The theoretical part contains literary research which is mainly focused on basic information for understanding the essence of the diploma thesis. The practical part is based on two questionnaire surveys between consumers and selected packaging free shops. The objective of these questionnaire surveys is to confirm or reject predetermined hypotheses. The work concludes with summarization and evaluation of whole situation about this problem on the Czech market

Cryptococcal Pneumonia: An Unusual Complication in a COVID-19 Patient

Cryptococcal superinfection is a rare but potentially fatal complication, especially if its detection and subsequent treatment are delayed. Histopathological findings of pulmonary parenchyma from a deceased patient with these complications were acquired. Quite interestingly, only a minimal inflammatory reaction could be seen in an individual with no previously known immune suppression, indicating a disturbance of the immune system. This finding was well in concordance with the described changes in cellular immunity in COVID-19. We report the case of a 60 year old male with critical coronavirus disease 2019 (COVID-19) complicated by cryptococcal pneumonia and multiorgan failure. Both X-ray and CT scans revealed lung infiltrates corresponding with COVID-19 infection early after the onset of symptoms. Despite receiving standard treatment, the patient progressed into multiple organ failure, requiring mechanical ventilation, circulatory support, and haemodialysis. Cryptococcus neoformans was detected by subsequent BAL, and specific antifungal treatment was instituted. His clinical status deteriorated despite all treatment, and he died of refractory circulatory failure after 21 days from hospital admission. Histopathological findings confirmed severe diffuse alveolar damage (DAD) caused by COVID-19 and cryptococcal pneumonia. Timely diagnosis of cryptococcal superinfection may be challenging; therefore, PCR panels detecting even uncommon pathogens should be implemented while taking care of critical COVID-19 patients