https://hdl.handle.net/20.500.12573/394 WoS Indexed Publications Collection 2026-07-16T03:03:24Z https://hdl.handle.net/20.500.12573/2541 Matching variants for functional characterization of genetic variants Cevik,Sabiha; Zhao,Pei; Zorluer,Atiyye; Pir, Mustafa S.; Bian, Wenyin; Kaplan, Oktay I. Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9. 2023-01-01T00:00:00Z https://hdl.handle.net/20.500.12573/2540 Integrating Biological Domain Knowledge with Machine Learning for Identifying Colorectal-Cancer-Associated Microbial Enzymes in Metagenomic Data Bakir-Gungor, Burcu; Ersoz, Nur Sebnem; Yousef, Malik Advances in metagenomics have revolutionized our ability to elucidate links between the microbiome and human diseases. Colorectal cancer (CRC), a leading cause of cancer-related mortality worldwide, has been associated with dysbiosis of the gut microbiome. This study aims to develop a method for identifying CRC-associated microbial enzymes by incorporating biological domain knowledge into the feature selection process. Conventional feature selection techniques often evaluate features individually and fail to leverage biological knowledge during metagenomic data analysis. To address this gap, we propose the enzyme commission (EC)-nomenclature-based Grouping-Scoring-Modeling (G-S-M) method, which integrates biological domain knowledge into feature grouping and selection. The proposed method was tested on a CRC-associated metagenomic dataset collected from eight different countries. Community-level relative abundance values of enzymes were considered as features and grouped based on their EC categories to provide biologically informed groupings. Our findings in randomized 10-fold cross-validation experiments imply that glycosidases, CoA-transferases, hydro-lyases, oligo-1,6-glucosidase, crotonobetainyl-CoA hydratase, and citrate CoA-transferase enzymes can be associated with CRC development as part of different molecular pathways. These enzymes are mostly synthesized by Eschericia coli, Salmonella enterica, Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, and Clostridioides dificile. Comparative evaluation experiments showed that the proposed model consistently outperforms traditional feature selection methods paired with various classifiers. 2025-01-01T00:00:00Z https://hdl.handle.net/20.500.12573/2539 Axial free vibration analysis of a tapered nanorod using Adomian decomposition method Coskun, Safa B.; Kara, Ozge; Atay, Mehmet T. This study aimed to conduct an analysis of the axial free vibration of tapered nanorods based on nonlocal elasticity theory. The small-scale effect on the free axial vibration of a tapered nanorod was studied employing the Adomian decomposition method (ADM) and the finite difference method (FDM) as a checking tool where a contradiction existed between the results of this study and available results in one highly cited work in the literature, which was used for comparison purposes in this work. Different boundary conditions for the nanorod were considered: fixed-fixed nanorod, fixed-free nanorod, and fixed-linear spring nanorod. The governing equation of the problem is a variable coefficient differential equation for which analytical solutions are strictly limited. For this type of problem, analytical approximate methods are effective, and there are many studies available in the literature on the application of these methods to solve linear/nonlinear ordinary/partial differential equations. ADM is one of the methods and was successfully used in this study to analyze the free vibration of nanorods. The results obtained in this study have shown that the presented technique is so powerful and has potential for applications in nanomechanics based on nonlocal elasticity theory. 2025-01-01T00:00:00Z https://hdl.handle.net/20.500.12573/2538 Horseradish peroxidase (HRP) nanoflowers-mediated polymerization of vinyl monomers Ozaydin, Gulbahar; Mirioglu, Muge; Kaplan, Naime; Dadi, Seyma; Ocsoy, Ismail; Gokturk, Ersen The effects of flower-shaped hybrid nano biocatalyst (hFe-NFs) from coordination between horseradish peroxidase (HRP) enzyme and Fe2+ ions on the free-radical polymerization reactions of three different vinyl monomers (styrene, methylmethacrylate and acrylamide) were investigated. Polymerizations of styrene and methylmethacrylate (MMA) were performed under emulsion conditions using three different surfactants in the presence of acetylacetone (AcAc) and hydrogen peroxide (H2O2) initiator. Polymerization of water soluble acrylamide was accomplished under surfactant-free media. According to the obtained outcomes, hFe-NFs exhibited higher catalytic activity towards polymerization of vinyl monomers compared to the free-HRP enzyme in terms of yields and the number average molecular weights (Mn) of the synthesized polymers. hFe-NFs also demonstrated very high thermal stability. While optimum polymerization of styrene was achieved at room temperature (RT), the highest polymerization yields for acrylamide and MMA were respectively accomplished at 70 and 60 degrees C in which free-HRP enzyme loses its catalytic activity. Preparation of the flower-shaped hFe-NFs, therefore, enables inexpensive and stable catalyst system for free-radical polymerization of vinyl monomers compared to free-HRP enzyme. Increasing catalytic activity and stability of hFe-NFs at higher reaction temperatures are very crucial for utilization of these types of catalysts in both scientific and industrial purposes. 2024-01-01T00:00:00Z