evolutionary analysis
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Background: Tuberculosis (TB) is a major cause of illness and death in many countries, especially in Asia and Africa. Repeated tests of microscopic examination are needed to be performed for early detection of the disease. Hence there is a need to automate the diagnostic process for improvement in the sensitivity and accuracy of the test. Objective: To automate the decision support system for tuberculosis digital images using histogram based statistical features and evolutionary based extreme learning machines. Materials and methods: The sputum smear positive and negative images recorded under standard image acquisition protocol are subjected to histogram based feature extraction technique. Most significant features are selected using student ‘t’ test. These significant features are further used as input to the differential evolutionary extreme learning machine classifier. Results: Results demonstrate that the histogram based significant features are able to differentiate TB positive and negative images with a higher specificity and accuracy. Conclusion: The methodology used in this work seems to be useful for the automated analysis of TB sputum smear images in mass screening disorders such as pulmonary tuberculosis.
2nd ed. xvi, 704 s., obr.
Parasites with wide host spectra provide opportunities to study the ecological parameters of speciation, as well as the process of the evolution of host specificity. The speciose and cosmopolitan louse genus Menacanthus comprises both multi-host and specialised species, allowing exploration of the ecological and historical factors affecting the evolution of parasites using a comparative approach. We used phylogenetic analysis to reconstruct evolutionary relationships in 14 species of Menacanthus based on the sequences of one mitochondrial and one nuclear gene. The results allowed us to validate species identification based on morphology, as well as to explore host distribution by assumed generalist and specialist species. Our analyses confirmed a narrow host use for several species, however in some cases, the supposed host specialists had a wider host spectrum than anticipated. In one case a host generalist (Menacanthus eurysternus) was clustered terminally on a clade almost exclusively containing host specialists. Such a clade topology indicates that the process of host specialisation may not be irreversible in parasite evolution. Finally, we compared patterns of population genetic structure, geographic distribution and host spectra between two selected species, M. eurysternus and Menacanthus camelinus, using haplotype networks. Menacanthus camelinus showed limited geographical distribution in combination with monoxenous host use, whereas M. eurysternus showed a global distribution and lack of host specificity. It is suggested that frequent host switching maintains gene flow between M. eurysternus populations on unrelated hosts in local populations. However, gene flow between geographically distant localities was restricted, suggesting that geography rather than host-specificity is the main factor defining the global genetic diversity of M. eurysternus.
- MeSH
- Amblycera klasifikace genetika fyziologie MeSH
- biologická adaptace MeSH
- biologická evoluce * MeSH
- fylogeografie * MeSH
- hostitelská specificita MeSH
- molekulární sekvence - údaje MeSH
- sekvenční analýza DNA MeSH
- tok genů MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
V roce 2009 uplynulo 200 let od narození Charlese Darwina a 150 let od vydání jeho nejznámějšího díla O vzniku druhů přírodním výběrem, neboli uchováním prospěšných plemen v boji o život. Soubor připravovaných statí, z nichž je tato první, se pokusí popsat, co evoluční teorie obnáší, jak se vyvíjela a co by o ní mohli vědět lékaři. Jestliže čteme výrok „evoluce je fakt, jehož výkladem je evoluční teorie“ je nutné, chceme-li předejít nedorozuměním, zabývat se jak pojmem fakt, tak pojmem teorie. Uvedený výrok užívá oba pojmy ve smyslu vědecký fakt a vědecká teorie. Úvodní stať se zabývá jejich obsahem i Darwinovou metodou.
The year 2009 was Darwin's anniversary year: Charles Darwin was born 1809 and his most famous book "on the origin of species by means of natural selection" appeared 1859. The collection of upcoming papers, this one is the first, will attempt to describe what biological evolution and evolutionary theory means, outline its history and pin point what physicians should probably know about evolution and evolutionary theory. If we accept the proposition: "evolution is the fact and evolutionary theory is its explanation", we must define the terms scientific fact and scientific theory in order to prevent misunderstandings. Darwin's working method is outlined.
- MeSH
- biologická evoluce MeSH
- fylogeneze MeSH
- molekulární evoluce MeSH
- Publikační typ
- úvodní články MeSH
Second edition x, 493. stran : grafy, ilustrace ; 24 cm
- MeSH
- behaviorální vědy MeSH
- biologická evoluce MeSH
- etologie MeSH
- fylogeneze MeSH
- vývojová biologie MeSH
- životní prostředí MeSH
- Konspekt
- Biologické vědy
- NLK Obory
- biologie
- NLK Publikační typ
- kolektivní monografie
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.
- MeSH
- fylogeneze MeSH
- ještěři genetika MeSH
- kur domácí genetika MeSH
- mitochondriální DNA genetika MeSH
- molekulární evoluce * MeSH
- pěnkavovití genetika MeSH
- plazi genetika MeSH
- pohlavní chromozomy genetika MeSH
- ptáci genetika MeSH
- Struthioniformes genetika MeSH
- želvy genetika MeSH
- zpěvní ptáci genetika MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Acta universitatis upsaliensis. Comprehensive summaries of Uppsala dissertations from the Faculty of Medicine, ISSN 0282-7476 923
58 s. : il. ; 25 cm
1st ed. xxiii, 622 s.
BACKGROUND: Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS: We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS: Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
