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    Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases
    (TAYLOR & FRANCIS, 2022) Öten, Ahmet Melih; Atak, Evren; Karaca, Banu Taktak; Fırtına, Sinem; Kutlu, Aslı
    Lipases and cellulases have been extensively used in the field of biotechnology for varied purposes. Mainly, the ongoing researches focus on the improvements of kinetic and enzymatic characteristics of enzymes to meet industrial needs. With the discovery of psychrophilic cellulase and lipase sources, a new era has opened for protein research by allowing the discovery of novel functions together with the description of unique cold adaptation mechanisms to harsh environments. The ability of cold-adapted lipase and cellulases to enable chemical reactions at lower temperatures provides a great opportunity to cut the cost of the finished product by lowering energy and purifying expanses. The advances in the cold-adapted lipase and cellulase enzymes are the cumulative efforts of organic chemists, biophysicists, biotechnologists, and process engineers who greatly contribute to a better understanding of cold-adaptation phenomena from different points of view. In this review, we cover the cold-adaptation aspects of cellulase and lipase enzymes from structural points of view by referring to the roles of Gly and Pro residues. Gly and Pro residues accelerate the cold-adaptation of enzymes by altering the conformational changes in the 3 D structure of proteins The list of microorganisms as a source of cold-adapted cellulases and lipases is given by referring to biotechnological applications. After introducing the thermodynamic background of Gly and Pro residues in the phenomena of cold-adaptation, specific examples are given to emphasise how introducing Gly and Pro into 3 D structure of protein molecules adds value in terms of biotechnological application by contributing to cold-adaptation
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    Identification of key genes and pathways for cholangiocarcinoma using an integrated bioinformatics analysis
    (Kare Publishing, 2022) Kutlu, Aslı; Arda, Merve; Atak, Evren; Ulukaya, Engin
    Objectives: The scope of this study was to identify potential genes as a promising biomarker in diagnosing cholangio-carcinoma (CCA) or differentiating the subtypes of CCA. In this study, we used Gene Expression Omnibus (GEO)-NCBI data sets as promising open sources to perform integrative analysis. Methods: The gene expression data sets of intrahepatic CCA (iCCA) and extrahepatic CCA (eCCA) were retrieved from GEO, and the statistical analysis of GSE45001 (iCCA), GSE76311 (iCCA), and GSE132305 (eCCA) was performed to identify significantly expressed genes. The association of listed genes with CCA was checked via text-mining approaches. For CCA, the details were provided by discussing its relations with our results. Then, the pathway analysis was performed to identify common pathways both in iCCA and eCCA. Results: The pathway analysis reveals that although there are common pathways between iCCA and eCCA, the associated genes within these pathways are different from one another. According to the results of upregulated gene sets, integrin cell surface interaction (R-HSA-216083), MET activates PTK2 signaling (R-HSA-8874081), degradation of the extracellular matrix (ECM) (R-HSA-1474228), nonintegrin membrane–ECM interaction (R-HSA-3000171), and assembly of collagen fibrils and other multimeric structures (R-HSA-2022090) are found as common pathways among these data sets, yet there is no reported common pathway within downregulated gene sets. A detailed study of common pathway analysis shows that COL1A1 and COL1A2 genes, whose associations with CCA have not been reported, seem promising to differentiate iCCA from eCCA. The pathway analysis also reveals that although there are common pathways between iCCA and eCCA, the associated genes within these pathways are different from one another. Conclusion: Focusing on pathways rather than genes is more promising for revealing the potential biomarkers to-gether with providing a deeper understanding by highlighting significant pathways. © 2022, Kare Publishing. All rights reserved.
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    Performing the comparative analysis to understand the functional roles of genes in different pathways of cardiomyopathy disease
    (Elsevier, 2021) Atak, Evren; Karaoğlu, Dilara; Serttürk, Seda; Koyuncu Irmak, Duygu; Yenenler-Kutlu, Aslı
    Personalized medicine is one of the popular approaches in biological sciences. Due to the great attention in personalized medicine, there exists a need for health decision algorithms developed through high-level pro-gramming languages that already compromised the statistical analyses and numerical computations. Here, we present a tool that enables us to facilitate making research in the PubMed database by classifying the scientific literature from the published abstracts and then performed the comparative analysis to highlight the importance of gene-variant relationships in the decision steps. After retrieving related genes from literature, we performed pathway analysis with them by using computer-based tools to differentiate these sub-pathways in cardiomy-opathy disease that are listed as hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathy. Then, the pathogenic variants existing in these genes at each sub-pathway are retrieved, and the mechanistic interpretation about them has been gained to explain more about the differences in genes’ mode of action. Lastly, the need of structure-based studies to explain the etiology of the disease has been emphasized by providing the protein structures of related genes as a guide. This study presents the importance of combining the text-mining approach with the bioinformatics tool in effective manner both for catching up with the updated literature and for revealing newly identified genes or pathways.