Fatma Aliye and Defense of Islamic Values

The article concerns an analysis of the recently published text by Fatma Aliye debating with European ideas and prejudices about Islam that has not been a subject of interest in the South Slavonic intellectual and academic circles. Fatma Aliye (1862–1936) was the first Turkish woman novelist, the first Turkish woman philosopher, and the author of the book Tezâhür-i Hakikat (Appearance of Truth) that was published for the first time in January 2016 on the occasion of the 80th anniversary of her death. Like some writers of the Tanzimat era, especially Namik Kemal, Fatma Aliye entered the debate with the European writers wishing to oppose the prevailing Orientalist approach in Europe that had been blaming Islam for the stagnation of sciences and culture. She demonstrated enviable erudition and devotion to the Islamic culture. Her views show the permanent duality of the Ottoman intellectuals between their desire for Westernization and their need to stay in the Islamic tradition. In many aspects, the approaches to Islam and the defence of Islamic values of Fatma Aliye are still current

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

<p>Abstract</p> <p>Background</p> <p>Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered.</p> <p>Results</p> <p>To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies.</p> <p>To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA.</p> <p>Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies.</p> <p>Conclusion</p> <p>Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.</p

Molecular evolution of cyclin proteins in animals and fungi

<p>Abstract</p> <p>Background</p> <p>The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi.</p> <p>Results</p> <p>We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution.</p> <p>Conclusions</p> <p>The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.</p

The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family

YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene transfer (HGT) from bacteria to the most recent common ancestor (MRCA) of land plants or to have inherited it from their ancestor, the charophyte algae. To refine YUCCA origin, we performed a phylogenetic analysis of the class B flavoprotein monooxygenases and comparative analysis of the sequences belonging to different families of this protein class. We distinguished a new protein family, named type IIb flavin-containing monooxygenases (FMOs), which comprises homologs of YUCCA from Rhodophyta, Chlorophyta, and Charophyta, land plant proteins, and FMO-E, -F, and -G of the bacterium Rhodococcus jostii RHA1. The type IIb FMOs differ considerably in the sites and domain composition from the other families of class B flavoprotein monooxygenases, YUCCAs included. The phylogenetic analysis also demonstrated that the type IIb FMO clade is not a sibling clade of YUCCAs. We have also identified the bacterial protein group named YUC-like FMOs as the closest to YUCCA homologs. Our results support the hypothesis of the emergence of YUCCA via HGT from bacteria to MRCA of land plants

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions-3

Ations, p < 0.001; d) negative correlations, p < 0.001. Whole analyzed 30 bp long region corresponds to [1;30] window of 29 dinucleotide positions. Also note that the SF-1 consensus sequence GTCAAGGTCA [39] located within region [10;19].<p><b>Copyright information:</b></p><p>Taken from "Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions"</p><p>http://www.biomedcentral.com/1471-2105/8/481</p><p>BMC Bioinformatics 2007;8():481-481.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2265442.</p><p></p

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions-5

Oint). Combined approach implied that both PWM and SiteGA models recognized a potential site.<p><b>Copyright information:</b></p><p>Taken from "Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions"</p><p>http://www.biomedcentral.com/1471-2105/8/481</p><p>BMC Bioinformatics 2007;8():481-481.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2265442.</p><p></p

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions-2

Is instance, better performance is marked by higher values and plots positioned further to the left. FP rates (X axis) are in logarithmic scale.<p><b>Copyright information:</b></p><p>Taken from "Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions"</p><p>http://www.biomedcentral.com/1471-2105/8/481</p><p>BMC Bioinformatics 2007;8():481-481.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2265442.</p><p></p

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions-4

<p><b>Copyright information:</b></p><p>Taken from "Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions"</p><p>http://www.biomedcentral.com/1471-2105/8/481</p><p>BMC Bioinformatics 2007;8():481-481.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2265442.</p><p></p