Striving for Higher University World Rankings: The Role of the Language Centre

There has been a long discussion in academia about crucial competencies of university graduates and factors which particular universities manage to perform better in the prestigious Times Higher Education World University Rankings (THE World University Ranking) or Academic Ranking of World Universities (ARWU, also called Shanghai Ranking) than the others. The role of university language centres (LC) has not been explored in this context, till now. This paper deals with a role of LCs as homes not only to language instruction but also as workplaces through which universities may become more successful institutions in terms of the rankings. A meaningful language policy (LP) is thus closely related to the future development of LCs beyond their current perceived role of a university language centre. This paper gives examples of language policy implementation steps while building on marketing principles for addressing target audience needs and communication. Drawing on the higher education institutions (HEI) priorities in terms of university rankings, the LCs´ natural role is to foster university communication culture, conditions for successful internalization and readiness to effectively communicate research results. The process of language policy implementation at the Language Centre of the University of Pardubice may provide an insight into the practice of a middle-size institution and illustrate the workplace emancipation process within an HE institution. Attention will be paid to general EU context as well as to tangible experience, implications of which may go beyond the limited space of one institution

Survey of extrachromosomal circular DNA derived from plant satellite repeats

<p>Abstract</p> <p>Background</p> <p>Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.</p> <p>Results</p> <p>We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (<it>Arabidopsis</it>, <it>Oryza</it>, <it>Pisum</it>, <it>Secale</it>, <it>Triticum </it>and <it>Vicia</it>). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.</p> <p>Conclusion</p> <p>This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.</p

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

BACKGROUND: Silene latifolia is a dioecious [corrected] plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. METHODOLOGY/PRINCIPAL FINDINGS: We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. CONCLUSIONS/SIGNIFICANCE: This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

The giant diploid faba genome unlocks variation in a global protein crop

Publisher Copyright: © 2023, The Author(s).Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.Peer reviewe

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes

Reflection of educational aims in LSP syllabi

The paper deals with traditional problem of ESP courses - big discrepancies in standards and competences of first year students at universities, which to a large degree restricts learning processes. Educational objectives are illustrated on an example of business English course for the students of the Faculty of Economics and Administration at University of Pardubice. As a possible way of improving the situation it gives an overview of educational objectives based on learning domains and practical examples of their application. Consequently derived key words are employed as a scheme for reviewing the syllabus and can provide the teachers with a checklist possibly functioning as criteria for evaluation and feedback

Analýza potřebvýznam a přínos analýzy potřeb pro zvýšení funkční gramotnosti

The paper deals with the needs, its importance and benefits for foreign language competence. This category has been viewed as one of the aspects of functional literacy and cosidered and indicator of the total level of education in a particular society. A need analysis being both a premise and a tool of an appropriate syllabus design deserves a systematic approach. As language teaching should focus on learner's needs (both current and future) a reflective syllabus design is a natural necessity. The paper drawing from the method of determining different roles of language users aspires to come up with a more complex way of assessing the learnes' language needs. Obviously, the merit of such an approach rests not only upon inter-curricular cooperation but also upon closer collaboration of the spheres of theory and practice, i.e. the tertiary level of education and labour market requirements. To proof all these mutual relations the paper offers both a few basic statistical data highlighting the level of the Czech society compared to other European countries in term of education and results of a language needs analysis carried among the Faculty of Economics and Administration students at Pardubice University. Key words: functional literacy, inter-curricular relations, theory - practise cooperation, self - reflection, deductive reasoning, autonomous learning

Profile of managers facilitating marketing management in chemical industry

Katedra ekonomiky a managementu chemického a potravinářského průmysluDokončená práce s úspěšnou obhajobo