PubMed İndeksli Yayınlar Koleksiyonu

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Activation of methane by Os+: Guided-ion-beam and theoretical studies
(CHEMM, 2013) Armentrout P.B.; Parke, Laura; Hinton, Christopher; Citir, Murat; 0000-0002-7957-110X; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Citir, Murat
Activation of methane by the third-row transition-metal cation Os + is studied experimentally by examining the kinetic energy dependence of reactions of Os+ with CH4 and CD4 using guided-ion-beam tandem mass spectrometry. A flow tube ion source produces Os+ in its electronic ground state and primarily in the ground spin-orbit level. Dehydrogenation to form [Os,C,2 H]++H2 is exothermic, efficient, and the only process observed at low energies for reaction of Os+ with methane, whereas OsH+ dominates the product spectrum at higher energies. The kinetic energy dependences of the cross sections for several endothermic reactions are analyzed to give 0K bond dissociation energies (in eV) of D0(Os+-C)=6.20±0. 21, D0(Os+-CH)=6.77±0.15, and D0(Os +-CH3)=3.00±0.17. Because it is formed exothermically, D0(Os+-CH2) must be greater than 4.71eV, and a speculative interpretation suggests the exothermicity exceeds 0.6eV. Quantum chemical calculations at the B3LYP/def2-TZVPP level show reasonable agreement with the experimental bond energies and with previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surfaces. Notably, the structure of the dehydrogenation product is predicted to be HOsCH+, rather than OsCH2+, in contrast to previous work.
Advances in Micelle-based Drug Delivery: Cross-linked Systems
(BENTHAM SCIENCE PUBL LTDEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer; 0000-0002-6887-6549; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü
There are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.
Aerial Swarms: Recent Applications and Challenges
(Springer, 2021) Mohamed Abdelkader; Samet Güler; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Güler, Samet
Purpose of review: Currently, there is a large body of research on multi-agent systems addressing their different system theoretic aspects. Aerial swarms as one type of multi-agent robotic systems have recently gained huge interest due to their potential applications. However, aerial robot groups are complex multi-disciplinary systems and usually research works focus on specific system aspects for particular applications. The purpose of this review is to provide an overview of the main motivating applications that drive the majority of research works in this field, and summarize fundamental and common algorithmic components required for their development. Recent findings: Most system demonstrations of current aerial swarms are based on simulations, some have shown experiments using few 10 s of robots in controlled indoor environment, and limited number of works have reported outdoor experiments with small number of autonomous aerial vehicles. This indicates scalability issues of current swarm systems in real world environments. This is mainly due to the limited confidence on the individual robot's localization, swarm-level relative localization, and the rate of exchanged information between the robots that is required for planning safe coordinated motions. Summary: This paper summarizes the main motivating aerial swarm applications and the associated research works. In addition, the main research findings of the core elements of any aerial swarm system, state estimation and mission planning, are also presented. Finally, this paper presents a proposed abstraction of an aerial swarm system architecture that can help developers understand the main required modules of such systems.
Air-stable, nanostructured electronic and plasmonic materials from solution-processable, silver nanocrystal building blocks
(American Chemical Society, 2014) Fafarman, Aaron T.; Hong, Sung-Hoon; Oh, Soong Ju; Caglayan, Humeyra; Ye, Xingchen; Diroll, Benjamin T.; Engheta, Nader; Murray, Christopher B.; Kagan, Cherie R.; 0000-0002-0656-614X; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Caglayan, Humeyra
Herein we describe a room-temperature, chemical process to transform silver nanocrystal solids, deposited from colloidal solutions, into highly conductive, corrosion-resistant, optical and electronic materials with nanometer-scale architectures. After assembling the nanocrystal solids, we treated them with a set of simple, compact, organic and inorganic reagents: ammonium thiocyanate, ammonium chloride, potassium hydrogen sulfide, and ethanedithiol. We find that each reagent induces unique changes in the structure and composition of the resulting solid, giving rise to films that vary from insulating to, in the case of thiocyanate, conducting with a remarkably low resistivity of 8.8 × 10-6 ·cm, only 6 times that of bulk silver. We show that thiocyanate mediates the spontaneous sintering of nanocrystals into structures with a roughness of less than 1/10th of the wavelength of visible light. We demonstrate that these solution-processed, low-resistivity, optically smooth films can be patterned, using imprint lithography, into conductive electrodes and plasmonic mesostructures with programmable resonances. We observe that thiocyanate-treated solids exhibit significantly retarded atmospheric corrosion, a feature that dramatically increases the feasibility of employing silver for electrical and plasmonic applications.
Alantolactone ameliorates graft versus host disease in mice
(ELSEVIER, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Şerife; Çakır, Mustafa; Özcan, Alper; Yılmaz, Ebru; Karakukcu, Musa; Donmez-Altuntas, Hamiyet; Yay, Arzu Hanim; Deniz, Kemal; Altay, Derya; Arslan, Duran; Canatan, Halit; Eken, Ahmet; Unal, Ekrem; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Kendirli, Perihan Kader
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naïve (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2–18 (n = 4) and non-GVHD patients between ages 2–50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naïve phenotype (CD62L+ CD44− ). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Analyzing the nexus between energy transition, environment and ICT: A step towards COP26 targets
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2023) Tzeremes, Panayiotis; Dogan, Eyup; Alavijeh, Nooshin Karimi; 0000-0003-0476-5177; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Doğan, Eyüp
In line with the Sustainable Development Goals and the recent COP26 summit, energy transition, low carbon emissions and technology have become extremely important subjects in the agenda of governments and poli-cymakers. The present study thus discusses the nexus between energy transition, economic growth, CO2 emis-sions and information and communications technology (ICT) in BRICS countries applying the novel GMM-PVAR method proposed on the annual data for the period 2000-2017. This method is strong to the issue of endogeneity which is commonly faced in the context of panel data analysis but mostly ignored in the literature. The findings of this research demonstrate that carbon emissions have a positive and significant effect on energy transition; similarly, raising economic growth augments the consumption of energy transition. Furthermore, ICT is found to be a significant choice in the development of energy transition and the solution of environmental challenges. Overall, technological factors in addition to economic and environmental factors also have great roles in the development of renewable energy and energy transition. Thus, results from this study call for government supports to develop ICT across the BRICS countries.
BODIPY-Based Semiconducting Materials for Organic Bulk Heterojunction Photovoltaics and Thin-Film Transistors
(WILEY-V C H VERLAG GMBH, POSTFACH 101161, 69451 WEINHEIM, GERMANY, 2019) Ho, Dongil; Ozdemir, Resul; Kim, Hyungsug; Earmme, Taeshik; Usta, Hakan; Kim, Choongik; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü;
The rapid emergence of organic (opto)electronics as a promising alternative to conventional (opto)electronics has been achieved through the design and development of novel pi-conjugated systems. Among various semiconducting structural platforms, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) pi-systems have recently attracted attention for use in organic thin-films transistors (OTFTs) and organic photovoltaics (OPVs). This Review article provides an overview of the developments in the past 10 years on the structural design and synthesis of BODIPY-based organic semiconductors and their application in OTFT/OPV devices. The findings summarized and discussed here include the most recent breakthroughs in BODIPYs with record-high charge carrier mobilities and power conversion efficiencies (PCEs). The most up-to-date design rationales and discussions providing a strong understanding of structure-property-function relationships in BODIPY-based semiconductors are presented. Thus, this review is expected to inspire new research for future materials developments/applications in this family of molecules.
Boron-rich amorphous boron oxides from ab initio simulations
(ELSEVIER, 2023) Karacaoglan-Çetin , Aysegul Ozlem; Durandurdu, Murat; 0000-0001-5636-3183; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Karacaoglan-Çetin, Aysegul Ozlem; Durandurdu, Murat
Amorphous boron oxide (BxO1-x, 0.5 ≤ x ≤ 95) configurations are simulated by means of an ab initio molecular dynamics technique and their microstructure and mechanical properties are revealed in details. With increasing B content, the average B-coordination noticeably increases from 3.18 to 5.62 whereas the O-coordination, surprisingly, remains almost null, about 2.0. The formation of complete B12 molecules is observed after 80% B concentrations. Chemical segregation is witnessed in most models and hence the resulting configurations show B: B2O3 phase separations. The mechanical properties (bulk, shear and Young moduli, Vickers hardness and microhardness) substantially increase with increasing B content. The amorphous materials (BxO1-x, x ≥ 80) are classified as hard materials. Within the limitations of DFT calculations and approaches used, we speculate that there is a ductile-to-brittle transition at around 70–75% B contents.
Building a challenging medical dataset for comparative evaluation of classifier capabilities
(ELSEVIER, 2024) Bozkurt, Berat; Coskun, Kerem; Bakal, Gokhan; 0000-0003-2897-3894; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bozkurt, Berat; Coskun, Kerem; Bakal, Gokhan
Since the 2000s, digitalization has been a crucial transformation in our lives. Nevertheless, digitalization brings a bulk of unstructured textual data to be processed, including articles, clinical records, web pages, and shared social media posts. As a critical analysis, the classification task classifies the given textual entities into correct categories. Categorizing documents from different domains is straightforward since the instances are unlikely to contain similar contexts. However, document classification in a single domain is more complicated due to sharing the same context. Thus, we aim to classify medical articles about four common cancer types (Leukemia, Non-Hodgkin Lymphoma, Bladder Cancer, and Thyroid Cancer) by constructing machine learning and deep learning models. We used 383,914 medical articles about four common cancer types collected by the PubMed API. To build classification models, we split the dataset into 70% as training, 20% as testing, and 10% as validation. We built widely used machine-learning (Logistic Regression, XGBoost, CatBoost, and Random Forest Classifiers) and modern deep-learning (convolutional neural networks - CNN, long short-term memory - LSTM, and gated recurrent unit - GRU) models. We computed the average classification performances (precision, recall, F-score) to evaluate the models over ten distinct dataset splits. The best-performing deep learning model(s) yielded a superior F1 score of 98%. However, traditional machine learning models also achieved reasonably high F1 scores, 95% for the worst-performing case. Ultimately, we constructed multiple models to classify articles, which compose a hard-to-classify dataset in the medical domain.
Can mesenchymal stem/stromal cells and their secretomes combat bacterial persisters?
(SPRINGER, 2023) Bicer-Çalışkan, Mesude; Fidan, Ozkan; 0000-0001-5312-4742; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Bicer-Çalışkan, Mesude; Fidan, Ozkan
The increasing number of life-threatening infections caused by persister bacteria is associated with various issues, including antimicrobial resistance and biofilm formation. Infections due to persister cells are often difficult to suppress without the use of last-resort antibiotics. Throughout the world, bacterial persistence and resistance create an unmet clinical demand for the exploration of newly introduced therapeutic approaches. Mesenchymal stem / stromal cells (MSCs) have an antimicrobial activity to protect against bacterial infections, including those caused by bacterial persisters. MSCs have substantial potential to secrete antimicrobial peptides (AMPs), including cathelicidin, beta-defensins, lipocalin-2, hepcidin, indoleamine 2,3-dioxygenase (IDO), cysteine proteases, and inducible nitric oxide synthases (iNOS). MSCs possess the potential to contribute to innate immunity by regulating the immune response. Recently, MSCs and their secreted components have been reported to improve antimicrobial activity. Bactericidal activity by MSCs and their secretomes has been shown to be mediated in part by the secretion of AMPs. Even though they were discovered more than 80 years ago, therapeutic options for persisters are restricted, and there is an urgent need for alternative treatment regimens. Hence, this review intends to critically assess the current literature on the effects of MSCs and their secretomes on persister bacteria. MSCs and their secretome-based therapies could be preferred as an up-and-coming approach to reinforce the antimicrobial efficiency in persister infections.
Capturing B type acute lymphoblastic leukemia cells using two types of antibodies
(WILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, 2019) Icoz, Kutay; Gercek, Tayyibe; Murat, Aysegul; Ozcan, Servet; Unal, Ekrem; AGÜ, Mühendislik Fakültesi, Elektrik & Elektronik Mühendisliği Bölümü;
One way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. (c) 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019
CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques
(ELSEVIER, 2024) Bakir-Gungor, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, Malik; 0000-0002-2272-6270; 0000-0002-2839-1424; 0009-0002-4373-8526; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bakir-Gungor, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre
Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2′ 3′ cyclic 3′ phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED.
Cell Proliferation and Cytotoxicity Assays
(BENTHAM SCIENCE PUBL LTDEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES, 2016) Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf
Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.
Cerium Oxide Nanoparticles Biosynthesized Using Fresh Green Walnut Shell in Microwave Environment and their Anticancer Effect on Breast Cancer Cells
(John Wiley and Sons Inc, 2022) Sulak, Mine; Turgut, Gurbet Celik; Sen, Alaattin; 0000-0002-8444-376X; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Sen, Alaattin
In this study, cerium oxide nanoparticles (CONPs) were synthesized using fresh green walnut shell extract in microwave environment. The morphology and structure of the CONPs were determined using ultraviolet-visible (UV/VIS), attenuated total reflection-Fourier transform infrared (ATR-FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray (EDX) spectroscopy, and scanning electron microscopy (SEM). Crystal purple staining, Annexin V-FITC detection, RT-PCR, P53, and NF-κB luciferase reporter assays were performed to evaluate the mechanism of action of CONPs in breast cancer cell lines (MCF7). The biosynthesized CONPs showed cytotoxic effects and induced apoptosis in MCF7 cells. Furthermore, CONPs induced P53 expression and suppressed NF-κB gene expression, both of which were confirmed using reporter assays. Based on the present results, it was concluded that CONPs can induce apoptosis by acting on P53 at the transcriptional level and may cause cell death by suppressing NF-κB-mediated transcription.
Computational Detection of Pre-microRNAs
(Humana Press Inc., 2022) Saçar Demirci, Müşerref Duygu; 0000-0003-2012-0598; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Saçar Demirci, Müşerref Duygu
MicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs is a vital element for investigating miRNA mediated posttranscriptional gene regulation machineries. Furthermore, experimental methods have challenging inadequacies in their capability to detect rare miRNAs, and are also limited to the state of the organism under examination (e.g., tissue type, developmental stage, stress-disease conditions). These issues have initiated the creation of high-level computational methodologies endeavoring to distinguish potential miRNAs in silico. On the other hand, most of these tools suffer from high numbers of false positives and/or false negatives and as a result they do not provide enough confidence for validating all their predictions experimentally. In this chapter, computational difficulties in detection of pre-miRNAs are discussed and a machine learning based approach that has been designed to address these issues is reviewed.
Computational prediction of microRNAs in Histoplasma capsulatum
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND, 2020) Demirci, Mueserref Duygu Sagar; 0000-0003-2012-0598; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü
MicroRNAs (miRNAs) are small and non-coding RNAs that regulate gene expression through post-transcriptional regulation. Although, the standard miRNA repository, MiRBase, lists more than 200 organisms having miRNA mediated regulation mechanism and thousands of miRNAs, there is not enough information about miRNAs of fungal species. Considering that there are various fungal pathogens causing disease phenotypes, it is important to search for miRNAs of those organisms. The leading cause of endemic mycosis in the USA is a fungal disease known as histoplasmosis, which is resulted by infection with a fungal intracellular parasite, Histoplasma capsulatum (H. capsulatum). In this work, genomes of H. capsulatum strains NAm1 and G217B were explored for potential miRNA like sequences and structures. Through a complex workflow involving miRNA detection and target prediction, several miRNA candidates of H. capsulatum and their possible targets in human were identified. The results presented here indicate that H. capsulatum might be one of the fungal pathogens having a miRNA based post-transcriptional gene regulation mechanism and it might have a miRNA mediated host - parasite interaction with human.
Development of a Nanoparticle-Embedded Chitosan Sponge for Topical and Local Administration of Chemotherapeutic Agents
(American Society of Mechanical Engineers (ASME), 2014) Goldberg, Manijeh; Manzi, Aaron; Aydin, Erkin; Singh, Gurtej; Khoshkenar, Payam; Birdi, Amritpreet; LaPorte, Brandon; Krauskopf, Alejandro; Powell, Geralle; Chen, Julie; Langer, Robert; 0000-0001-7811-2959; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Aydin, Erkin
The following work describes the development of a novel noninvasive transmucosal drug delivery system, the chitosan sponge matrix (CSM). It is composed of cationic chitosan (CS) nanoparticles (NPs) that encapsulate cisplatin (CDDP) embedded within a polymeric mucoadhesive CS matrix. CSM is designed to swell up when exposed to moisture, facilitating release of the NPs via diffusion across the matrix. CSM is intended to be administered topically and locally to mucosal tissues, with its initial indication being oral cancer (OC). Currently, intravenous (IV) administered CDDP is the gold standard chemotherapeutic agent used in the treatment of OC. However, its clinical use has been limited by its renal and hemotoxicity profile. We aim to locally administer CDDP via encapsulation in CS NPs and deliver them directly to the oral cavity with CSM. It is hypothesized that such a delivery device will greatly reduce any systemic toxicity and increase antitumor efficacy. This paper describes the methods for developing CSM and maintaining the integrity of CDDP NPs embedded in the CSM.
Dicarboxylic Acids Induced Tandem Transformation of Silver Nanocluster
(AMER CHEMICAL SOC, 2023) Wang, Zhi; Gupta, Rakesh Kumar; Alkan, Fahri; Han, Bao-Liang; Feng, Lei; Huang, Xian-Qiang; Gao, Zhi-Yong; Tung, Chen-Ho; Sun, Di; 0000-0002-4046-9044; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Alkan, Fahri
Structural transformation of metal nanoclusters (NCs) is of great ongoing interest regarding their synthesis, stability, and reactivity. Although sporadic examples of cluster transformations have been reported, neither the underlying transformation mechanism nor the intermediates are unambiguous. Herein, we have synthesized a flexible 54-nuclei silver cluster (Ag54) by combining soft (t BuC�C−) and hard (n PrCOO−) ligands. The existence of weakly coordinated n PrCOO− enhances the reactivity of Ag54, thus facilitating the dicarboxylic acid to induce structural transformation. X-ray structural analyses reveal that Ag54 transforms to Ag28 cluster-based 2D networks (Ag28a and Ag28b) induced by H2suc (succinic acid) and H2glu (glutaric acid), whereas with H2pda (2,2′-(1,2-phenylene)diacetic acid), a discrete Ag28 cluster (Ag28c) is isolated. The key intermediate Ag17 that emerges during the self-dissociation of Ag54 was isolated by using cryogenic recrystallization and characterized by X-ray crystallography. The “tandem transformation” mechanism for the structure evolution from Ag54 to Ag28a is established by time-dependent electrospray ionization mass spectrometry (ESIMS) and UV−vis spectroscopy. In addition, the catalytic activity in the 4-nitrophenol reduction follows the sequence Ag28c > Ag28b > Ag28a > Ag54 due to more bare silver sites on the surface of the Ag28 cluster unit. Our findings not only open new avenues to the synthesis of silver NCs but also shed light on a better understanding of the structural transformation mechanism from one cluster to another or cluster-based metal−organic networks induced by dicarboxylates.
Differential in vitro anti-leukemic activity of resveratrol combined with serine palmitoyltransferase inhibitor myriocin in FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) carrying AML cells
(SPRINGER, 2022) Ersoz, Nur Sebnem; Adan, Aysun; 0000-0003-3343-9936; 0000-0002-3747-8580; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Ersoz, Nur Sebnem; Adan, Aysun
Treatment of FMS-like tyrosine kinase 3 (FLT3)-internal tandem duplication (ITD) AML is restricted due to toxicity, drug resistance and relapse eventhough targeted therapies are clinically available. Resveratrol with its multi-targeted nature is a promising chemopreventive remaining limitedly studied in FLT3-ITD AML regarding to ceramide metabolism. Here, its cytotoxic, cytostatic and apoptotic effects are investigated in combination with serine palmitoyltransferase (SPT), the first enzyme of de novo pathway of ceramide production, inhibitor myriocin on MOLM-13 and MV4-11 cells. We assessed dose-dependent cell viability, flow cytometric cell death and cell cycle profiles of resveratrol in combination with myriocin by MTT assay, annexin-V/PI staining and PI staining respectively. Resveratrol's dose-dependent effect on SPT protein expression was also checked by western blot. Resveratrol decreased cell viability in a dose- dependent manner whereas myriocin did not affect cell proliferation effectively in both cell lines after 48h treatments. Although resveratrol induced both apoptosis and a significant S phase arrest in MV4-11 cells, it triggered apoptosis and non-significant S phase accumulation in MOLM-13 cells. Co-administrations reduced cell viability. Increased cytotoxic effect of co-treatments was further proved mechanistically through induction of apoptosis via phosphatidylserine relocalization. The cell cycle alteration in co-treatment was significant with an S phase arrest in MV4-11 cells, however, it was not effective on cell cycle progression of MOLM-13 cells. Resveratrol also increased SPT expression. Overall, modulation of SPT together with resveratrol might be the possible explanation for resveratrol's action. It could be an integrative medicine for FLT3-ITD AML after investigating its detailed mechanism of action in relation to de novo pathway of ceramide production.
Discovery of a C-S lyase inhibitor for the prevention of human body malodor formation: tannic acid inhibits the thioalcohol production in Staphylococcus hominis
(SPRINGER NATURE LINK, 2025) Fidan, Ozkan; Karipcin, Ayse Doga; Kose, Ayse Hamide; Anaz, Ayse; Demirsoy, Beyza Nur; Arslansoy, Nuriye; Sun, Lei; Mujwar, Somdutt; 0000-0001-5312-4742; 0009-0005-7132-842X; 0009-0008-5514-8711; 0000-0003-4037-5475; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Fidan, Ozkan; Karipcin, Ayse Doga; Kose, Ayse Hamide; Anaz, Ayse; Demirsoy, Beyza Nur; Arslansoy, Nuriye
Human body odor is a result of the bacterial biotransformation of odorless precursor molecules secreted by the underarm sweat glands. In the human axilla, Staphylococcus hominis is the predominant bacterial species responsible for the biotransformation process of the odorless precursor molecule into the malodorous 3M3SH by two enzymes, a dipeptidase and a specific C-S lyase. The current solutions for malodor, such as deodorants and antiperspirants are known to block the apocrine glands or disrupt the skin microbiota. Additionally, these chemicals endanger both the environment and human health, and their long-term use can influence the function of sweat glands. Therefore, there is a need for the development of alternative, environmentally friendly, and natural solutions for the prevention of human body malodor. In this study, a library of secondary metabolites from various plants was screened to inhibit the C-S lyase, which metabolizes the odorless precursor sweat molecules, through molecular docking and molecular dynamics (MD) simulation. In silico studies revealed that tannic acid had the strongest affinity towards C-S lyase and was stably maintained in the binding pocket of the enzyme during 100-ns MD simulation. We found in the in vitro biotransformation assays that 1 mM tannic acid not only exhibited a significant reduction in malodor formation but also had quite low growth inhibition in S. hominis, indicating the minimum inhibitory effect of tannic acid on the skin microflora. This study paved the way for the development of a promising natural C-S lyase inhibitor to eliminate human body odor and can be used as a natural deodorizing molecule after further in vivo analysis.

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