Yazar "Yilmaz, Alper" seçeneğine göre listele

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    Comparative analysis of retrosynthesis applications for predicting of pathways for plant Secondary metabolite production
    (Taylor & Francis Ltd, 2024) Yonet, Nilay; Yuka, Selcen Ari; Turker, Musa; Yilmaz, Alper
    Secondary metabolites (SMs), organic compounds synthesized by plants, play crucial roles in their own physiology and within their ecological niches, and have extensive usages in industries like pharmaceuticals, cosmetics, and food. Due to the complex nature of these metabolites, utilizing microorganisms has been proposed for their efficient and cost-effective production. In addressing challenges in SM synthesis, retrosynthesis has become essential. Applications such as RetroPath2.0, BioNavi-NP, and RetroBioCat have been developed to predict and design biosynthetic pathways, supporting synthetic biology and metabolic engineering efforts. These applications employ different methodologies to enhance the synthesis of target compounds, yet often face limitations in user-friendliness, functionality, and adaptability. This study evaluates the potential of RetroPath2.0, RetroBioCat, and BioNavi-NP in predicting the production pathways of 11 alkaloids, a class of plant secondary metabolites (PSMs). Through comparative analysis, the efficacy of these applications in proposing alternative production strategies was assessed. Findings highlighted RetroPath2.0's capability in outlining precise production pathways in host organisms, despite some restrictions in its broader practicability. The study also demonstrated the production pathways of dimethyltryptamine, nicotine, and higenamine in non-plant hosts, illustrating the practical uses of these applications.
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    Öğe
    The role of ceRNAs in breast cancer microenvironmental regulation and therapeutic implications
    (Springer Heidelberg, 2025) Yilmaz, Alper; Yuka, Selcen Ari
    The tumor microenvironment, which is the tailored physiological milieu of heterogeneous cancer cell populations surrounded by stromal and immune cells as well as extracellular matrix components, is a leading modulator of critical cancer hallmarks and one of the most significant prognostic indicators in breast cancer. In the last few decades, with the discovery of the interactions of ncRNAs with diverse cellular molecules, considerable emphasis has been devoted to understanding their direct and indirect roles in specific functions in breast cancer. Collectively, all of these have revealed that the competitive action of protein-coding RNAs and ncRNAs such as circRNAs and lncRNAs, which have a shared affinity for miRNAs, play a vital role in the molecular regulation of breast cancer. This phenomenon, termed as competing endogenous RNAs (ceRNAs), facilitates modeling the microenvironment through intercellular shuttles. Microenvironment ceRNA interactions have emerged as a frontier in the deep understanding of the complex mechanisms of breast cancer. In this review, we first discuss cellular ceRNAs in four key biological processes critical for microenvironmental regulation in breast cancer tissues: hypoxia, angiogenesis, immune regulations, and ECM remodeling. Further, we draw a complete portrait of microenvironment regulation by cell-to-cell cross-talk of shuttled ceRNAs and offer a framework of potential applications and challenges in overcoming the aggressive phenotype of the breast cancer microenvironment.