Development of inverse sub-domain method for boundary conditions computation of heat conduction

V technické praxi je velmi důležité vyvíjet výpočetně efektivní a zároveň přesné a stabilní numerické metody pro řešení úloh přenosu tepla a hmoty. Tato práce se zaměřuje na inverzní úlohu vedení tepla, která je potřebná k výpočtům okrajových podmínek (teploty, tepelného toku nebo součinitele přenosu tepla). V dnešní době jsou k výpočtu inverzní úlohy používané sekvenční metoda a metoda pro výpočet celé domény. V této diplomové práci je vyvinut nový přístup k inverzní úloze, tzv. sub-doménová metoda, ve které dochází k vyzdvižení výhod a naopak potlačení nevýhod obou známých metod. Součástí práce je i testování všech zmíněných přístupů k inverzní úloze na vygenerovaných datech a datech z reálných experimentů. Dále je tato nová metoda porovnávána s oběma známými metodami, a to jak vzhledem k přesnosti výsledků, tak i vzhledem k výpočtové náročnosti.It is very important to develop efficient but still accurate and stable numerical methods for solving heat and mass transfer processes in many industrial applications. The thesis deals with an inverse heat conduction problem which is used to compute boundary conditions (temperatures, heat flux or heat transfer coefficient). Nowadays, two approaches are often used for inverse task - sequential estimation and whole domain estimation. The main goal of this work is to develop a new approach, the so-called sub-domain method, which emphasizes advantages just as reduce disadvantages of both methods mentioned above. This approach is then tested on generated prototypic data and on data from real experiments. All methods are compared with respect to accuracy of results as well as to computational efficiency.

Approximation of the cooling effects of water nozzles by mathematical functions

Bakalářská práce se zabývá chlazením vodními tryskami s kuželovým rozstřikem. V práci je uveden princip procesu plynulého odlévání oceli, během kterého se tyto trysky velmi často využívají. Dále jsou vysvětleny základní mechanismy přenosu tepla a průběh chlazení ostřikem. Je zde rovněž shrnut postup při experimentálním měření chladicích účinků těchto trysek. Cílem práce je pak nalézt vhodnou 3D matematickou funkci, která by popisovala rozložení součinitele přestupu tepla pod tryskou, a sestavit algoritmus pro určení parametrů této funkce. Celý model je naprogramován v prostředí MATLAB a je implementován na vzorová měřená data pro dva typy trysek.The Bachelor thesis deals with a cooling process of full cone water nozzles. It explains the principle of the continuous steel casting which these nozzles are used for. The basics of heat transfer and spray cooling are also described. The thesis then summarizes the way of the experiment with these nozzles. The purpose of the thesis is to choose an appropriate 3D mathematical function which would well characterize the distribution of the heat transfer coefficient under the nozzle and then create an algorithm for finding its parameters. The algorithm is programmed in MATLAB and implemented on the data gained by the experimental way for two types of full cone water nozzles.

Molecular Profiling of Acute and Chronic Rejections of Renal Allografts

Both antibody mediated (AMR) and T-cell mediated (TCMR) rejections either acute or chronic represent the main reason for late graft dysfunction. In this study we aimed to evaluate differences in the intrarenal expression patterns of immune system related genes in acute and chronic rejections. Graft biopsies were performed and evaluated according to Banff classification. Using the TaqMan Low Density Array, the intrarenal expressions of 376 genes relating to immune response (B-cell activation, T-cell activation, chemokines, growth factors, immune regulators, and apoptosis) were analyzed in the four rejection categories: chronic AMR, chronic TCMR, acute AMR, and acute TCMR. The set of genes significantly upregulated in acute TCMR as compared to acute AMR was identified, while no difference in gene expressions between chronic rejections groups was found. In comparison with functioning grafts, grafts that failed within the next 24 months after the chronic rejection morphological confirmation presented at biopsy already established severe graft injury (low eGFR, higher proteinuria), longer followup, higher expression of CDC20, CXCL6, DIABLO, GABRP, KIAA0101, ME2, MMP7, NFATC4, and TGFB3 mRNA, and lower expression of CCL19 and TRADD mRNA. In conclusion, both Banff 2007 chronic rejection categories did not differ in intrarenal expression of 376 selected genes associated with immune response

A multi gene sequence-based phylogeny of the Musaceae (banana) family

<p>Abstract</p> <p>Background</p> <p>The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.</p> <p>Results</p> <p>The 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera and <it>Musa </it>sections. Nucleotide variation within the sample confirmed the close relationship of <it>Australimusa </it>and <it>Callimusa </it>sections and showed that <it>Eumusa </it>and <it>Rhodochlamys </it>sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution of <it>Musa </it>to ~50 Mya. The first estimates for the divergence times of the four <it>Musa </it>sections were also obtained.</p> <p>Conclusions</p> <p>The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.</p

Karyotype differentiation in cultivated chickpea revealed by Oligopainting fluorescence in situ hybridization

Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies

An Increasing Need for Productive and Stress Resilient Festulolium Amphiploids:What Can Be Learnt from the Stable Genomic Composition of Festuca pratensis subsp. apennina (De Not.) Hegi?

Genome composition of Festuca pratensis subsp. apennina (De Not.) Hegi, a tetraploid fescue species native to the tall forbs communities of south-eastern Europe at altitudes between 1100 and 2200m a.s.l. has been the subject of some debate by grass taxonomists. Our cytogenetic analyses including fluorescence in situ hybridisation with probes for genomic DNA and selected DNA repeats revealed the species to be allotetraploid and derived from interspecific hybridization between F. pratensis Huds., a species confined to grassland at lower altitudes, and a so far unknown Festuca species. Besides tetraploids, triploids and pentaploids were found growing in Alpine meadows in close association with F. pratensis subsp. apennina. Triploid cytotypes predominated at many sites in Switzerland and Romania, and in some localities, they were the only cytotypes observed. Cytogenetic analyses revealed the triploids to be hybrids between diploid F. pratensis and tetraploid Festuca pratensis subsp. apennina, while the pentaploid cytotypes originated from hybridization between F. pratensis subsp. apennina and hexaploid F. arundinacea Schreb., a closely-related species growing in a close vicinity to F. pratensis subsp. apennina. Parental genomes of F. pratensis subsp. apennina and of the triploid and pentaploid hybrids showed no evidence of homoeologous chromosome pairing and interspecific recombination, supporting previous observation of a disomic inheritance at meiosis, where chromosome pairing was restricted to bivalent associations. A hypothesis is presented that a chromosome pairing regulator(s), reported previously in other polyploid broad-leaved fescue species of the Festuca subg. Schedonorus, is present and functional in F. pratensis subsp. apennina. It is likely that a common ancestors’ genome that carries the chromosome pairing regulator(s) is present in all polyploid broad-leaved fescue species, and its acquisition was a key event that enabled speciation, and development of a polyploid series within Festuca. Identification of a functional chromosome pairing regulator capable of stabilizing advantageous genome combinations in hybrids within the Lolium-Festuca complex would greatly assist in development of stable Festulolium cultivars. Its expression within Festulolium amphiploid cultivars would assist strategies aimed at climate-proofing productive European grasslands to combat exposures to stress conditions

New chromosome counts and genome size estimates for 28 species of Taraxacum sect. Taraxacum

The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T. sect. Ruderalia; T. officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia. The chromosome number of the 28 species (T. aberrans Hagendijk, Soest &amp;amp; Zevenbergen, 1974, T. atroviride Štěpánek &amp;amp; Trávníček, 2008, T. atrox Kirschner &amp;amp; Štěpánek, 1997, T. baeckiiforme Sahlin, 1971, T. chrysophaenum Railonsala, 1957, T. coartatum G.E. Haglund, 1942, T. corynodes G.E. Haglund, 1943, T. crassum H. Øllgaard &amp;amp; Trávníček, 2003, T. deltoidifrons H. Øllgaard, 2003, T. diastematicum Marklund, 1940, T. gesticulans H. Øllgaard, 1978, T. glossodon Sonck &amp;amp; H. Øllgaard, 1999, T. guttigestans H. Øllgaard in Kirschner &amp;amp; Štěpánek, 1992, T. huelphersianum G.E. Haglund, 1935, T. ingens Palmgren, 1910, T. jugiferum H. Øllgaard, 2003, T. laticordatum Marklund, 1938, T. lojoense H. Lindberg, 1944 (= T. debrayi Hagendijk, Soest &amp;amp; Zevenbergen, 1972, T. lippertianum Sahlin, 1979), T. lucidifrons Trávníček, ineditus, T. obtusifrons Marklund, 1938, T. ochrochlorum G.E. Haglund, 1942, T. ohlsenii G.E. Haglund, 1936, T. perdubium Trávníček, ineditus, T. praestabile Railonsala, 1962, T. sepulcrilobum Trávníček, ineditus, T. sertatum Kirschner, H. Øllgaard &amp;amp; Štěpánek, 1997, T. subhuelphersianum M.P. Christiansen, 1971, T. valens Marklund, 1938) is 2n = 3x = 24. The DNA content ranged from 2C = 2.60 pg (T. atrox) to 2C = 2.86 pg (T. perdubium), with an average value of 2C = 2.72 pg. Chromosome numbers are reported for the first time for 26 species (all but T. diastematicum and T. obtusifrons), and genome size estimates for 26 species are now published for the first time

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

© 2016, The Author(s). Bananas (Musa spp.) are one of the main fruit crops grown worldwide. With the annual production reaching 144 million tons, their production represents an important contribution to the economies of many countries in Asia, Africa, Latin-America and Pacific Islands. Most importantly, bananas are a staple food for millions of people living in the tropics. Unfortunately, sustainable banana production is endangered by various diseases and pests, and the breeding for resistant cultivars relies on a far too small base of genetic variation. Greater diversity needs to be incorporated in breeding, especially of wild species. Such work requires a large and thoroughly characterized germplasm collection, which also is a safe depository of genetic diversity. The largest ex situ Musa germplasm collection is kept at the International Transit Centre (ITC) in Leuven (Belgium) and currently comprises over 1500 accessions. This report summarizes the results of systematic cytological and molecular characterization of the Musa ITC collection. By December 2015, 630 accessions have been genotyped. The SSR markers confirmed the previous morphological based classification for 84% of ITC accessions analyzed. The remaining 16% of the genotyped entries may need field verification by taxonomist to decide if the unexpected classification by SSR genotyping was correct. The ploidy level estimation complements the molecular data. The genotyping continues for the entire ITC collection, including newly introduced accessions, to assure that the genotype of each accession is known in the largest global Musa gene bank. Open Access ispartof: Biodiversity and Conservation vol:26 issue:4 pages:801-824 status: publishe

Chromosome painting facilitates anchoring reference genome sequence to chromosomes In Situ and integrated karyotyping in banana (Musa Spp.)

Open Access Journal; Published online: 20 Nov 2019Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis “DH Pahang” to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae