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Metastatik prostat kanserinde PCBB ve IVD genlerinin ekspresyon analizi
Prostate cancer is a leading cause of cancer-related mortality among men worldwide. It demonstrates variable biological behavior ranging from localized indolent forms to highly metastatic and treatment-resistant stages. Understanding the molecular mechanisms responsible for this progression is essential for improving diagnosis and therapeutic strategies. The present study focused on the expression analysis of PCBB and IVD genes in prostate cancer cell lines representing different stages of disease progression. Human prostate cancer cell lines PC3 (CRL-1435™, metastatic, androgen-independent) and LNCaP (CRL-1740™, androgen-dependent) were used as experimental models. Total RNA was extracted, quantified, and converted into complementary DNA (cDNA) for quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The comparative gene expression analysis revealed that PCBB expression was significantly reduced in PC3 cells compared to LNCaP, indicating a potential relationship between PCBB downregulation and the metastatic phenotype of prostate cancer. In contrast, IVD expression showed no statistically significant difference between the two cell lines, suggesting that its transcription remains stable regardless of disease stage. Statistical analysis was conducted using GraphPad Prism and significance was determined at p < 0.05, p < 0.01, p < 0.001, and p < 0.0001. The findings demonstrate that PCBB may play a role in the metabolic or molecular changes associated with prostate cancer metastasis, while IVD expression appears unaffected. These results contribute to the growing understanding of gene-specific regulation in prostate cancer and may guide further studies exploring their diagnostic and prognostic potential.
Investigating the role of COL1A1 and FN1 gene expression in cisplatin-resistant ovarian cancer
Ovarian cancer (OC) is a fatal malignancy that has been attributed majorly to the emergence of chemoresistance. Cisplatin is a first-line treatment, but its resistance is one of the main clinical challenges. This study examined how two extracellular matrix (ECM) genes; COL1A1 and FN1 play a role in cisplatin-resistant ovarian cancer. We examined gene expression in the A2780 human ovarian carcinoma cell line and its cisplatin resistant counterpart (A2780-R) through quantitative real-time PCR (qRT-PCR). The results of our study demonstrated that the genes were significantly downregulated in the resistant cells. The reduced expression of FN1 and COL1A1 observed in cisplatin-resistant ovarian cancer cells may indicate a cell-specific adaptive mechanism, potentially shaped by differences in cisplatin dosage or exposure patterns that modify extracellular-matrix gene regulation. Because both the amount and scheduling of cisplatin administration influence cellular responses, variations in dosing regimens may affect how resistance emerges and ultimately shape therapeutic outcomes. It shows that there is a previously underestimated resistance mechanism that should be examined.
Raman spectroscopic and microscopic analysis of tissue type, molecular composition, and glioblastoma identification in brain tissue sections
Glioblastoma (GB) is the most common primary malignant brain tumor. Despite improvements in treatments, survival probability has remained shorter than 2 years for most patients over the last 20 years. Accurate diagnosis of GB requires pathological evaluation of the tumor tissues using light microscopy, along with routine or specialized staining. Recent research also identified significant genetic/epigenetic alterations that influence diagnosis, prognosis, and treatment in addition to routine pathological evaluation. Identification requires the tissue to be sampled many times and analyzed using different methods that require additional time, resources, and expertise. To determine whether the tissue used for routine analysis can also be used to perform more detailed and comprehensive analysis without staining, we propose to use Raman Spectroscopy (RS), which is a label-free and non-destructive technique. RS provides molecule-specific spectra from the chemical composition of the sample for rapid analysis. In this thesis, we investigated GB, white matter (WM), gray matter (GM), and necrosis (NC) regions of GB patients using RS to determine whether a similar precision can be achieved as the routine histomorphologic diagnostic process. First, we proposed a refined protocol for effectively clearing paraffin from Formalin-Fixed Paraffin-Embedded brain tissue sections, without destroying the sample morphology and chemical composition, for eliminating the substantial Raman spectra of paraffin. We demonstrated that the less expensive and less toxic clearing agent CleareneTM removes paraffin as effectively as p-Xylene, the mostly used clearing agent in histopathology laboratories. Thus, we suggest substituting CleareneTM with p-Xylene for deparaffinization of brain tissue sections for Raman spectral analysis. Second, we optimized the choice of Raman spectrum acquisition parameters (excitation wavelength, acquisition time, accumulation count,), tissue thickness, and Raman substrate type (CaF2, glass). Third, we acquired the Raman spectra of GB, WM, GM, and NC regions and analyzed the spectral profile regarding the Raman peaks given in the literature. Raman spectra of GB and WM regions (nGB = 20, nWM = 18), which were annotated by an expert neuropathologist, have been classified with 87.2±1% GB and 90.7±1% WM training/test accuracies using machine learning models (SVM, kNN, RF). The effect of pre-processing of Raman spectra on classification accuracies has been investigated. Sample preparation conditions, Raman acquisition protocols, and machine learning classification models showed a successful proof-of-concept demonstration for the proposed Raman-based GB identification workflow. While there is room for further refining the machine learning models for improved training and validation accuracies, these protocols could be improved for eventual clinical utility. Once the clinical applicability and refined classification accuracies are demonstrated, these protocols might assist neuropathologists in error-free identification of GB in the clinics.
Calcium signal modulation based on the photo electrical stimulation of voltage-gated ion channels in cancer cells enables a novel approach in cancer therapy
Photoelectrical stimulation of cells with bioelectronic interfaces embedded with semiconductor organic polymers has been shown promising applications in neuroprosthetics such as retinal prothesis. Photoelectrical stimulation of the cell membranes activates voltage-gated ion channels through photoelectrical charge separation mechanism in the semiconductor materials and it can alter intracellular calcium level. On the other hand, targeting voltage gated ion channels in cancer cells to induce cell apoptosis through calcium signaling alternation is an effective mechanism which has been explained before. In this regards, remote control of the voltage-gated ion channels aimed to alter intracellular calcium by using photo-active organic polymers can be a novel technology in cancer therapy. In this thesis, we used p type semiconductor structure (ITO (Indium thin oxide)/P3HT (poly(3-hexylthiophene-2,5-diyl)) and pn (ITO/ ZnO (Zinc oxide)/ P3HT) photovoltaic junctions to stimulate breast cancer cells. We showed that the photostimulation of electrically excitable breast cancer cells through photocapacitive currents generated by the photovoltaic junctions are able to excite the cells and alternate intracellular calcium based on the calcium imaging experiments, and it can induce apoptosis and necrosis at low light treatment properties (10 mW/ Cm2 green light intensity, and 50ms light durations). MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] cell viability test for MDA-MB-231 cells showed 20-30% cell death for ITO/ P3HT and 51-60% cell death for ITO/ZnO/P3HT samples (under 24hr light treatment with 10mW/cm2 light intensity, 50ms pulse duration, and 3Hz frequency). In addition, Annexin V and PI fluorescent staining showed both apoptosis and necrosis for treated cells grown on top of the ITO/P3HT substrate. Moreover, western blot analysis proved the activation of the Poly (ADP-ribose) polymerase (PARP) for the treated MDA-MB-231 cells grown on top of the ITO/P3HT substrates which indicates PARP mediated cell death. Based on the results that we report in this thesis, photoelectrical stimulation of cells (through long time overstimulation) can induce cell apoptosis and necrosis in cancer cells.
Development of an open-architecture process control system for the direct metal laser sintering (DMLS)
Do˘grudan metal lazer sinterleme (DMLS) i¸slemi kullanılarak metal par¸caların katmanlı imalatı, geometrik olarak karma¸sik modelleri imal etmek i¸cin toz malzemenin katman bazında eritilmesini kullanır. Burada, y¨uksek g¨u¸cl¨u bir lazer ı¸sını, metal toz katmanındaki tarama vekt¨orleri boyunca hareket ettirilir ve bu, biti¸sik malzeme ile birle¸sen bir eriyik havuzunun olu¸sturulmasıyla sonu¸clanır. Tipik olarak, DMLS makineleri pahalıdır ancak hassas metal par¸calar ¨uretmek i¸cin eklemeli ¨uretim se¸cenekleri. Di˘ger avantajlar daha az malzeme israfı, iyile¸stirilmi¸s ¨ur¨un geli¸stirme d¨ong¨us¨u, hızlı prototipleme, ¨ozelle¸stirmeler ve i¸slevsel olarak derecelendirilmi¸s metalin k¨u¸c¨uk parti boyutlu ¨uretimi par¸calar. Bu ¨ozellikler, havacılık i¸cin uygun bir se¸cim olan DMLS s¨urecini, ¨ozelle¸stirme gerektiren otomotiv, di¸s, alet ve tıp end¨ustrileri d¨u¸s¨uk toplu ¨uretim. Orne˘gin, ortopedik implantların imalatı DMLS, gerekli ¨ozelle¸stirmeyi ¨ sunar ve her iki hastaya da fayda sa˘glayan ¨ozelliklere izin verir ve cerrahlar. Bununla birlikte, bu hassas metal katkılı imalatın avantajları teknolojinin hala k¨u¸c¨uk ve orta ¨ol¸cekli end¨ustrilerde ¸co˘galması gerekmektedir. y¨uksek maliyeti, par¸ca kalitesi sorunları ve bireysel yapılar arasında d¨u¸s¨uk tutarlılık. Metalik ¨ur¨unler ¨uretmeye y¨onelik DMLS se¸cene˘ginin, genel s¨ure¸c zinciri boyunca yayılan teknik zorluklarla birlikte geldi˘gi belirtilmektedir. Aslında, metal tozlarının imalatı sırasında ve s¨uper ala¸sımlar, 50'den fazla i¸slem parametresi vardır son b¨ol¨um¨un kalitesini etkilemek i¸cin etkile¸simde bulunan. Burada birincil odak noktası, par¸calı eritme sırasında metalik tozların karma¸sık termal davranı¸sı, her bir katmandaki sınır ko¸sullarına ba˘glı olarak i¸slem parametrelerinin dikkatli bir ¸sekilde se¸cilmesini gerektirir. Bu nedenle, DMLS tabanlı eklemeli ¨uretim teknolojisi, kapsamlı par¸ca kalitesini etkileyen bu s¨ure¸c parametrelerini tasarlamak i¸cin ara¸stırma yapın ve tekrarlanabilirlik. Aynı zamanda, ara¸stırma odaklı deneyler yapmak i¸cin a¸cık eri¸simli makine platformu ve yazılım deste˘gi mevcut de˘gildir. Bu nedenle, metal tozunun erimesini ke¸sfetmenin zorlu˘gu, b¨uy¨uk ¨ol¸c¨ude esas olarak end¨ustriyel kullanım i¸cin satılan ticari sistemler. Bu sistemler sadece pahalı olmakla kalmaz, aynı zamanda temel operasyonlara ¸cok sınırlı eri¸sim sunar ve donanımları, dolayısıyla kullanıcı i¸cin bir kara kutu gibi g¨or¨unmektedir. Bu zorlu˘gun ¨ustesinden gelmek i¸cin, kullanıcıyla birlikte b¨uy¨uyebilen a¸cık eri¸simli bir ara¸stırma platformu sistemi kabul edilir i¸se yarar. Bu ara¸stırmada, MarcSLM adlı a¸cık kontrol mimarili bir DMLS sistemi geli¸stirilmi¸stir. ˙I¸s, MarcSLM makine mekanizmasının geli¸stirilmesini i¸cerir, sistem kontrol yazılımı ve olu¸sturulmu¸s s¨ure¸c planlama yazılımı. Bu sistem metroloji sens¨orleri i¸cin mod¨uler eri¸sim ve aray¨uz sa˘glamak ¨uzere tasarlanmı¸stır. altta yatan eritme s¨urecini yakalamada faydalıdır. Bu ama¸cla, ilk olarak, metalik katmanlı ¨uretim dijital ipli˘gi i¸cin bir ¸cer¸ceve ¨onerilmi¸stir. Bu i¸slem zincirinin ayrı mod¨uller dizisi olarak g¨or¨unmesini sa˘glayarak derleme i¸slemcisi ve sistem kontrol yazılımının yazılım uygulaması. Mod¨uller, imalat tarafından sıkı testlerin yapıldı˘gı bir ¸calı¸san makineye entegre edilir numune modelleri ba¸sarıyla y¨ur¨ut¨ulm¨u¸st¨ur. Daha da geli¸stirmek i¸cin yerle¸sik i¸slemci yazılımının i¸slevselli˘gi, manip¨ulasyon h¨ukm¨u dikme tabanlı kafes yapıları da dahildir. Bu h¨ucresel manifoldlar ¸cok maksimum avantaj elde etmeyi sa˘glayan katmanlı imalat tasarımında kullanı¸slıdır DMLS teknolojisinin. Geli¸stirilen model kompakt bir veri kullanır kafesleri i¸slemek i¸cin yapı ve azaltılmı¸s hesaplamayla verimli do˘grudan dilimleme sunar makine bilgisayarında uygulanabilmesi i¸cin maliyet. Ayrıca, bu ¸calı¸smanın bir par¸cası olarak kafeslerin tasarlanması i¸cin yapısal topoloji optimizasyonuna dayalı yeni bir y¨ontem ¨onerilmi¸stir. T¨um derleme verileri ¨ozelle¸stirilmi¸s bir makine i¸slemlerini sorunsuz bir ¸sekilde t¨uretmek i¸cin tasarlanmı¸s makine kodu.
Design, fabrication and characterization of light-responsive functionalized hydrogel for tissue engineering applications
Stimuli-responsive hydrogels have gained immense consideration due to the unique properties such as spectacular volume transition in response to a variety of physical and chemical stimuli. These hydrogels have been particularly effective, considering exceptional degree of authority over material properties because of external signals. The precise control over the hydrogel properties resulted in significant advancements in medical devices and improved methodologies for tissue engineering applications. In this thesis, we aimed to develop biocompatible and biodegradable stimuli-responsive hydrogels for tissue engineering applications. Different methods of hydrogel fabrication were studied throughout the study such as free radical photopolymerization and photodimerization reactions. In the first part of the thesis, we pursued the conventional method of hydrogel formation where polymers were functionalized with light-sensitive anthracene. Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barriers for clinical translation of these materials. We reported the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels lead to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two- and five-fold with anthracene conjugation during photopolymerization and photodimerization, respectively. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to the anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision. Further, we reported the synthesis of single and dual-crosslinked anthracene-functional chitosan-based hydrogels in the absence of toxic initiators. Single crosslinking was achieved through dimerization of anthracene, whereas dual-crosslinked hydrogel was formed through dimerization of anthracene and free radical photopolymerization of methacrylated-chitosan in the presence of non-toxic initiator riboflavin, a well-known vitamin B2. Both single and dual-crosslinked hydrogels were found to be elastic, as was determined through rheological analysis. We observed that the dual-crosslinked hydrogels exhibited higher Youngs modulus than the single-crosslinked hydrogels, where the modulus for single and dual-crosslinked hydrogels were measured as 9.2±1.0 kPa and 26±2.8 kPa, respectively resulting in significantly high volume of cells in dual-crosslinked hydrogel (2.2x107 µm3) compared to single-crosslinked (4.9x106 µm3). Furthermore, we investigated the cytotoxicity of both hydrogels towards 3T3-J2 fibroblast cells through CellTiter-Glo assay. Finally, immunofluorescence staining was carried out to evaluate the impact of hydrogel modulus on cell morphology. This study comprehensively presents functionalization of chitosan with anthracene, uses nontoxic initiator riboflavin, modulates the degree of crosslinking through dimerization of anthracene and free radical photopolymerization, and further modulates cell behavior through the alterations of hydrogel properties. In the second part of the thesis, a novel technique was introduced and photocrosslinked hydrogels were synthesized from natural and synthetic polymers in the absence of any photoinitiator or coinitiator. Very simple and facile method was developed to synthesize biocompatible and non-toxic hydrogels through free-radical polymerization. The potential of the developed procedure is shown against natural and synthetic polymers both. For this, acrylated forms of alginate, chitosan, gelatin, hyaluronic acid, and polyethylene glycol (PEG) were used and mechanically robust hydrogels were developed under UV (365 nm) and visible (430 nm) light as determined through rheological analysis. We also observed that the UV light-crosslinked hydrogels exhibited higher crosslinking and showed high Youngs modulus as compared to visible light-crosslinked hydrogels. Cell viability analysis shows that the developed hydrogels are non-toxic towards fibroblast cells. The biomedical potential of these hydrogels was further explored by encapsulating the two model cell lines where NIH-3T3 fibroblast cells and bone-marrow derived mesenchymal stem cells (rBM-MSCs) were encapsulated in the hyaluronic acid (HA)-based hydrogel. The enhanced growth rate of the cells shows that the crosslinking procedure is non-toxic to the cells. Scope of this study was further expanded to sustained release of therapeutics. DOX was successfully loaded into HA-based hydrogel. The maximum loading was observed as 97% and an accelerated release rate was seen in visible light-based crosslinked hydrogel due to the open pore structure compared to the UV-based hydrogel. Another potential application for such initiator-free hydrogel might be the vascularization which was also explored in this part of the thesis. Engineering of organized vasculature is a key step in the improvement of functional and clinically relevant tissue constructs. Various hydrogel-based culture systems are used to make in vitro models for angiogenesis. Here, we developed initiator-free photocrosslinked gelatin-based hydrogels under UV (365 nm) and visible light (430 nm) for the tubular formation of functional vascular networks. Detailed rheological analysis revealed that Gel-MA hydrogels were robust and viscoelastic in nature. We tuned the mechanical properties of Gel-MA hydrogel depending on the type of exposed light. By this way, we obtained stiff and soft Gel-MA hydrogels. Immunofluorescence labeling was used to track the impact of hydrogel modulus over the cell shape and tubular formation. We found higher tubular formation in soft Gel-MA hydrogel compared to the stiff hydrogel. Further, we also investigated the tubular formation in the presence and absence of growth factors and found that tubular formation was much higher in the presence of growth factors as expected. The cytotoxicity of the developed hydrogel was evaluated towards HUVECs by using the CellTiter-Glo assay and found to be non-toxic.
Emergence of large-scale order in bacterial active matter
During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects and microdomains. These structures may benefit bacterial strains, providing invasive advantages during colonization. Active matter dynamics of growing colonies drives the emergence of these ordered structures. However, additional biomechanical factors also play a significant role during this process. Here we show that the velocity profile of growing colonies creates strong radial orientation during inward growth when crowded populations invade a closed area. During this process, growth geometry sets virtual confinement and dictates the velocity profile. Herein, flow-induced alignment and torque balance on the rod-shaped bacteria significantly differed, resulting in new stable orientational equilibrium in the radial direction. Our analysis revealed that the dynamics of these orientational defects depend on bacterial length and can promote the survival of the longest bacteria around localized nutritional hot spots. The present results indicate a new mechanism underlying structural order and provide mechanistic insights into the dynamics of bacterial growth on complex surfaces.
Novel implant designs and surgical guidelines in orthopaedics
Orthopaedic fractures and their treatments are creating an increasing burden on the healthcare system. With the rise of global life expectancy and the elderly population, fractures related to low bone strength are becoming ever more common and the proper medical management of fractures is becoming more important. The goal in fracture management is to safely restore the original anatomy of the fractured bone and mobilize the patient for return to the original life quality. To advance the current fracture fixation technology and surgical intervention procedures, novel implant designs and surgical guidelines using computational methods are proposed in this thesis in three different sub-fields of orthopaedics. For the fixation of long bone shaft fractures, the traditional monolithic nature of bone plates is challenged, and adjustable locking and modular plate designs are investigated. For proper implementation of the femoral head implants to avoid possible hip joint penetration complications, the established fluoroscopic distance-based risk predictors, tip-apex and tip-surface distances, have been revised and an algorithm is developed for assessing the safety of the inserted guidewire or cephalomedullary screw for intraoperative utilization. Finally, for median sternotomy closure operation, polymer coating over the traditional stainless-steel cerclage is proposed to alleviate the possible lateral sternal cut-through damage in high-risk patients and the application and optimization of superelastic nitinol staples for sternal closure is discussed.
Androgen receptor-dependent enhancers in prostate cancer
Prostate cancer is one of the leading causes of cancer-related death in European men. In almost all patients, Androgen Receptor (AR)-mediated transcription is critical for the development and proliferation of cancer. Upon activation, the AR binds to DNA and induces the expression of genes essential for cellular differentiation and tumor growth. AR-mediated transcription is driven by distal regulatory enhancer elements that control gene expression by looping to gene promoters. However, there are exponentially more AR binding sites than differentially expressed genes. It is unknown how these regions work to induce transcription. Delineating the regulatory logic of AR-mediated transcription is critical to understanding how this transcription factor drives prostate cancer growth and progression. To identify these specific AR enhancers, we functionally tested all clinical AR binding sites with a massively multi-parallel enhancer assay to create the first "map" of AR transcriptional activity. From this, we found that only a subset of ARBS had functional enhancer activity AR. Those AR-regulated enhancers act as a regulatory hub that frequently cooperates with other ARBS to drive transcription. Yet intriguingly, we observed that many of the minimal enhancer activity sites are often required for gene transcription, suggesting that ARBS have different functions that are independent of only enhancer activity. To explore this, we systematically characterized the KLK gene locus and found that AR occupancy is dependent on other AR binding sites in the same transcriptional network. Overall, this work provides fundamental insights into AR functions to drive gene activation.
Novel 3D composite polymeric scaffolds for tissue engineering
3D printed poly(lactic acid) (PLA) grids coated with electrospun PLA, chitosan and silk fibroin webs or their composites were fabricated and evaluated for liver tissue engineering applications. United States Food and Drug Administration (FDA) approved biodegradable and biocompatible PLA was chosen for mechanical strength and ease of processibility. It was shown that simple fused deposition method or 3D printing can be used to create not only rigid but also soft structures by changing the printing parameters, without the use of complex procedures or hardware, to match the mechanical properties of soft tissues. As PLA is inherently not cell binding, effect of surface modification by treatment with sodium hydroxide to improve hydrophilicity and cell attachment was investigated. Soft 3D printed PLA grids with 1x1, 3x3 and 5x5 mm pore sizes were produced. PLA webs were also deposited on these grids by electrospinning using various solvent combinations. Effect of fiber surface topographies on wettability, cell attachment and cell viability was investigated. Furthermore, grids were also coated with electrospun PLA/chitosan and PLA/silk fibroin webs to improve cell viability. Calcium modified silk fibroin was blended with PLA and used for liver tissue engineering for the first time in this study. 3D composite scaffolds produced were characterized in terms of surface topography and roughness using Scanning Electron Microscopy (SEM) and White Light Interferometry (WLI) respectively. Wettability was assessed by static water contact angle measurements. Materials were also characterized by FTIR-ATR spectroscopy and XRD measurements. Hep2G cell viability and cell growth was investigated by MTT assay. The cell growth on the scaffolds were demonstrated by SEM imaging. Strong protein adsorption on scaffolds after immersing in DMEM with and without serum protein were shown by SEM images and water contact angle measurements. Biodegradation tests were performed by immersing the scaffolds in PBS and DMEM with serum for 3 weeks. Through these investigations we tried to correlate material type and surface properties and cell viability. Our results indicate that 3D printed PLA grids coated with various electrospun webs were all bioactive and may be suitable for long term in vitro liver tissue modelling and liver tissue engineering applications. Keywords : Liver tissue engineering, 3D bioactive scaffolds, surface modification
Developing a novel recombinant IL-1 receptor antagonist to treat the cytokine storm in Covid-19
One of the deadliest symptoms of Covid-19 is the development of acute respiratory distress syndrome (ARDS) in the patients. The hyperactivation of immune system due to SARS-CoV-2 infection results in the sudden release of numerous cytokines including interleukins which is called cytokine storm. Interleukin-1β (IL-1β) is known as one of the most important cytokines playing a role in the emergence of this phenomenon in inflammatory diseases. Therefore, blocking the pathway induced by IL-1β has been considered a promising treatment approach in the presence of cytokine storm. Endogenous interleukin-1 receptor antagonist (IL-1Ra) binds to the same receptor as IL-1β and inhibits the pathway. The commercially available recombinant version of IL-1Ra, anakinra, has already been used in the treatment of autoinflammatory diseases such as rheumatoid arthritis (RA), type II diabetes, and familial Mediterranean fever (FMF) since 2001 in order to alleviate the inflammatory response. Therefore, it has been used on Covid-19 patients in clinical trials and shown to be a potential medication due to its role in the attenuation of the cytokine storm. In the first part of this thesis, in vitro characterization of two novel recombinant IL-1Ra proteins was performed. The recombinant proteins were produced by Dr. Cem Albayrak's and Dr. Serdar Uysal's group as local alternatives to anakinra, which is not commercially available in Turkey. In this part of the thesis, the bioactivity of the recombinant proteins and their effects on cell viability were investigated. In order to assess the bioactivity of the proteins, genetically modified HEK-Blue cells were used to determine the impact of the proteins in IL-1β-induced SEAP production using QUANTI-Blue agent to measure, and IC50 value was calculated. Also, the ability of IL-1Ra-His6 protein to inhibit IL-1β-induced IL-6 production in MRC-5 lung fibroblasts was evaluated via ELISA. Finally, the viability of HEK293T and MRC-5 cells were inquired using CTG assay. Chitosan is one of the most promising biomaterials due to its unique properties such as biocompatibility, biodegradability, mucoadhesivity, and low immunogenicity. These properties make chitosan an excellent candidate for various biomedical applications such as wound healing, tissue engineering, and gene/drug delivery. Using chitosan in nanoparticle-based delivery systems increases its potential even further, primarily enabling the delivery of a high amount of genetic material. In the second part of the thesis, transfection and permeation enhancing capabilities of TRAIL encapsulated PEGylated chitosan nanoparticles were investigated. 5 kDa PEG was used to PEGylate chitosan to improve its physicochemical properties. Nanoparticles were synthesized using a crosslinking agent (TPP) and PEGylated chitosan derivative. In order to encapsulate tumor necrosis factor (TNF) α-related apoptosis-inducing ligand (TRAIL) inserted plasmid DNA was added in the process of crosslinking. Synthesized nanoparticles were characterized using scanning electron microscopy (SEM). Also, TRAIL encapsulated nanoparticles were incubated with 3 different glioblastoma (GBM) cell lines (A172, LN18, T98G), and transfection efficiencies of nanoparticles were experimentally investigated using flow cytometry. For the assessment of permeation enhancing capability of nanoparticles, Calu-3 cells were used, and the change in the transepithelial electrical resistance (TEER) was measured.
A computational study on pathogenic exon-1 Huntington fragment fiber structure and its nucleation
Huntington is a genetic disease linked with the expansion of the poly glutamine (polyQ) sequence in the Huntington (htt) protein. It is known that when the length of the polyQ block exceeds 36, the N-terminal exon-1 fragment of htt protein self assembles into fibrils in patients' brains. The aggregation mechanism of exon-1 into fibrils and the structural details of the fibril are still not fully understood. Two of the most plausible mechanisms remain to be the N-terminal flanking domain httNT α-helix driven aggregation and membrane mediated aggregation. The structure of the exon-1 fragment inside the fiber consists of an amphiphatic α helix from the httNT , a compact core made up of polyQ β-hairpins, and an extended proline rich domain (PRD). On the contrary, isolated httNT and short polyQ domains in solution display an intrinsically disordered character. Understanding the conformational transition of these domains from the disordered state, to the structure in the fiber remains an outstanding question. This thesis work is organized into three chapters. In chapter three, we investigate the chain length dependence of polyQ secondary structure by using molecular dynamics simulations. Our analysis show that α-helical structures favored by short molecules are replaced by mixed structures with α and β character as polyQ length increases. In chapter four, we study the structure of the polyQ block within the fiber to construct a model in agreement with the experimental findings. Our computational model indicates that only the correlated behavior of χ1 and χ3 dihedral angles leads to the bimodal χ1 distribution observed in experiments. Furthermore, the bimodal χ angle distribution is essential for the formation of the steric zipper motif and the extended side chain blocks connected via hydrogen bonds in the polyQ block. Finally, by applying this model to the exon-1 fragment we test the viability of the α helical httNT block within the fiber structure. In the fifth chapter, we analyze the interaction of the httNT block with a membrane and its influence on the polyQ block's conformation and aggregation. We observe that the httNT fragment adopts a fully extended α-helical structure inside the membrane, but unlike bulk water it does not self associate. This strong anchoring by httNT leads to an increased concentration of polyQ blocks on the membrane surface. Comparison of the β-sheet vs. sandwich models of polyQ seeds, suggests that the steric zipper motif is key for further nucleation.
Investigation of public single cell transcriptomics datasets to identify disease-related cellular phenotypes and molecular alterations of perivascular cells in multiple sclerosis
OBJECTIVE: In this thesis research, we aimed to investigate the molecular changes that occur in perivascular cells during Multiple Sclerosis, specifically pericytes and fibroblasts. For this purpose, bioinformatic tools are utilized to analyze the publicly available single-cell RNA sequencing datasets. METHODS: Firstly, we replicated the analysis presented in the "A human brain vascular atlas reveals diverse mediators of Alzheimer's risk" by Yang et al. to hold a view into molecular characteristics of mural cells in humans. Then, we analyzed the data presented in the article named "A lymphocyte–microglia–astrocyte axis in chronic active multiple sclerosis" by Absinta et al. We focused on the vascular cell cluster that was not studied in the article. We isolated this cluster from the other cells and then subclustered to study the characteristics of mural cells and fibroblasts in chronic MS lesions. In both studies the datasets are provided as fasq files. Our workflow has 9 steps including quality control, normalization, feature selection, dimensionality reduction, integration, 2-dimensional embedding, clustering, differential gene expression, and gene set enrichment analysis. RESULTS: First, the UMAP and t-SNE graphs were generated. Then, the identity of each cluster was determined according to the marker genes that are highly expressed by these cells in differential gene expression analysis. Marker genes were shown on UMAP graphs. Differentially expressed genes in mural cells, fibroblasts and endothelial cells were shown with volcano plots. KEGG pathway analysis was performed to identify the cellular pathways that are enriched in specific cell types. CONCLUSIONS: In the dataset of Absinta et al., sub-clustering of the vascular cluster (Cluster 11 and 13) revealed that this cluster is actually a combination of endothelial cells, pericytes, vascular smooth muscle cells, fibroblasts and a small contaminating population of oligodendrocytes. In the fibroblast cluster, enrichment of fibrosis related genes including Loxl4, Col12a1, Col15a1, Col6a3, Col11a1, Col13a1, FBN1, Col1a2 and Col1a1 was striking, and these genes were not described in the Alzheimer's disease dataset. DGE analysis of mural cell cluster revealed enriched expression of mostly the marker genes and several signaling pathways. KEY WORDS: Bioinformatics, single-cell RNA sequencing, Multiple Sclerosis, pericytes, fibroblasts
Thermoplastic microfluidics for 3D cell culturing
Microfluidic platforms have recently become essential in cell studies since they can closely mimic the 3D cell culture environment. These platforms need to have hydrophilic, transparent, and biocompatible properties. Material selection, fabrication method, and bonding type are critical for biomedical studies to achieve these purposes. This thesis has focused on polydimethylsiloxane (PDMS)and polymethyl methacrylate (PMMA) as materials for the formation of microfluidic chips with unique physical and chemical properties. The first part of the thesis focuses on PDMS chips produced by the soft lithography method and cell studies performed with these chips. In the second part, the leading research is based on the solvent bonding technique for forming PMMA chips. We did surface analyzes to investigate the quality of microfluidic platform building with thermoplastics. We found optimum parameters for temperature and solvent type for bonding PMMA microfluidics. The final version of this platform has allowed the creation of a functional environment for 3D cell culture work.
Machine Learning-enabled optimization of microneedle design for interstitial fluid collection
Utilization of microneedles (MNs) for biological fluid sampling and drug delivery is an emerging field in biotechnology, which contributes greatly to non-invasive methods in medicine. Prior studies on MNs propose designs based on mechanical testing and optimize physical parameters of the MN based on trial-and-error method. While these methods show adequate results, it is possible to enhance the performance of a MN using a large dataset of parameters and their respective performance using advanced data analysis methods. Machine learning (ML) is an important field of study in data analytics that mimics human learning behavior. It is one of the most studied topics in computational sciences which expedites various decision-making processes in many different areas, including biotechnology. In this study, an integration of finite element analysis and ML models are proposed with the purpose of determining the best physical parameters for a MN design, in order to maximize the amount of collected fluid. The fluid behavior in a MN patch is simulated with several different physical and geometrical parameters using COMSOL Multiphysics®, and the resulting dataset is used as the input for ML algorithms including multiple linear regression, random forest regression, decision tree regression, support vector regression, and neural networks. As a comparable method, iterative optimization is performed via LiveLink™ for MATLAB®. This study essentially introduces a novel approach to optimizing MN design for predetermined performance metrics.
Novel InP-based quantum dots via ZnO shelling and ruthenium doping for lighting and antibacterial applications
Semiconductor colloidal quantum dots (QDs) have been at the focus of attention in recent years due to their advantageous properties, including emission tunability by quantum confinement effect and material composition, high photoluminescence quantum yield (PLQY), and chemical stability. Thus, QDs are regarded as ideal materials for a wide variety of applications such as light-emitting diodes (LEDs) and photocatalysis. In the first part of our thesis, we demonstrated highly efficient quasi-type-II InP/ZnO/ZnS core/shell QDs with a PLQY of 91%. It is generally accepted perspective that type-II core/shell QDs, in which electron and hole wavefunctions are spatially separated, exhibit low PLQY. Even though type-II QDs with high PLQY values have been reported recently, they consist of heavy metals which show toxic effects. In our study, we used environmentally benign InP-based QDs as an alternative material compared to cadmium counterparts. After the synthesis of InP core QDs, we grew ZnO shell by thermal decomposition process to obtain type-II heterostructure. Subsequently, multiple ZnS shells were grown by SILAR technique. We integrated as-synthesized core/shell QDs on blue LED die using a novel architecture in liquid-state to minimize the host material effect. The resulting QD-LED exhibited external quantum efficiency (EQE) of 9.4%. In the second part of thesis, we introduced for the first-time ruthenium doping into InP/ZnS QDs as alternative strategy for efficient red-emitters. To date, various transition metals doping into InP QDs have been investigated, however, ruthenium (Ru) ion doping into InP QDs has not been explored yet. In our study, we synthesized Ru doped InP QDs by hot injection of ruthenium precursor into main solution at elevated temperature. Ru presence was confirmed by optical and structural analysis techniques. Ru doped InP-based QDs displayed higher PLQY in the red spectral region compared to undoped sample. The integration of Ru-doped QDs into LEDs in a liquid matrix led to an external quantum efficiency of 7.9%. In the last part of thesis, we investigated the potential of InP/ZnO core/shell QDs with type-II band alignment as a novel antibacterial agent. To date, various types of colloidal QDs have been introduced for antibacterial applications, including InP, ZnO, and CdTe. However, antibacterial activity of the type-II based QDs have not been studied yet. In our study, we demonstrated that InP/ZnO QDs exhibited reactive oxygen species (ROS) generation, including superoxide (•O2⁻) and hydroxyl radicals (•OH). Furthermore, upon low intensity green light stimulation (3 mW.cm-2) the optimized core/shell QDs displayed high antibacterial activity of 99% inhibition against Pseudomonas aeruginosa. These findings showed novel InP-based QDs via ZnO shelling and ruthenium doping are efficient material for LED and antibacterial applications.
Fabrication of a biodegradable piezoelectric-based wearable sensor for non-invasive monitoring of dynamic human motions and physiological signals
Recent advancements in flexible sensors and piezoelectric materials have facilitated the progress of continuous monitoring systems in the form of wearable and implantable medical devices, enabling the monitoring of human physiological signals. However, the non-degradable nature of these materials has resulted in the accumulation of significant amounts of electronic waste (e-waste) and necessitated subsequent surgeries for device removal. In this study, we introduce a flexible and biodegradable piezoelectric material fabricated specifically for wearable and implantable devices. This material addresses the issues associated with secondary surgeries and e-waste while providing a high-performance platform for the continuous and seamless monitoring of human physiological signals and tactile stimuli. The innovative combination of bioresorbable poly (L-lactic acid) (PLLA) and glycine has resulted in the development of flexible piezoelectric devices capable of non-invasive measurement of artery pulse signals in near-surface arteries and detecting slight muscle movements, including those of the trachea, esophagus, and joints. Furthermore, we demonstrate the complete degradability of the piezoelectric film in a phosphate buffer saline (PBS) solution at a temperature of 37°C. The pressure sensor derived from this material exhibits a high sensitivity of 13.2 mV/kPa, with a response time of 10 ms, and demonstrates excellent mechanical stability. Additionally, this piezoelectric material showcases comparable performance to commonly used non-degradable counterparts for measuring physiological signals. Due to its degradable nature, it can also be employed in temporary implantable medical devices for monitoring purposes.
Holografik ekran kullanan intraoküler lens temelli görüntü simülatörü
Cataract is defined as the cloudiness of the crystalline lens structure due to aging, trauma, etc. It is one of the most common preventable eye diseases in the world. The only treatment is surgery. During the surgery, the cataractous lens is removed and an artificial intraocular lens is implanted into the eye. There is an ongoing research effort to improve intraocular lens optical characteristics and depth-of-field to make patients totally spectacle-free after cataract surgery. However, modeling the vision through a cataractous lens and demonstrating various intraocular lens options before surgery are both significant challenges. In the first part of this thesis research, we developed an eye model to assess the performance of different intraocular lens options. Furthermore, we used the results of the eye model in a custom holographic vision simulator developed in our group to predict the postoperative vision of patients before surgery. In the clinical assessments, we employed a computational holographic display as it is the only technology that can generate digitally programmable exit pupils and simultaneously display content at different depths. Our artificial eye model was used to evaluate the optical performance and the point spread functions of different intraocular lenses. Those PSFs were then used to compute phase holograms to display on our custom holographic vision simulator. We characterized three different intraocular lenses using a standardized resolution target and point light source illumination using an light emitting diode. Monofocal, bifocal, and trifocal intraocular lenses exhibited a contrast decrease of 5%, 42%, and 45% and a resolution limit of 4.49, 4.00, and 4.00 lp/mm at 35cm (using 8% modulation transfer function criteria), respectively. Monofocal intraocular lenses had the best resolution and contrast. The multifocal lenses produced prominent photic phenomena such as halos and glare around bright light sources, reducing contrast and resolution. We compared our results with the literature and confirmed that the visual functions of intraocular lenses could be successfully modeled and simulated using a holographic display before surgery. In the second part of this research, we used our eye model and developed a cataractous lens simulator for progressive levels of opacification, which is achieved by applying a reversible chemical procedure on the intraocular lens surfaces. After the lens is fully or partially immersed in acetone, subsequent testing of the lens in distilled water results in a progressive change in opacification level within minutes. We objectively measured the quality of vision by obtaining modulation transfer function curves, transmission, and spectroscopic measurements at different opacification levels. By simulating variable opacification across the IOLs, we tested how vision changes from less dense to more dense cataractous regions in a holographic display system with programmable small exit pupils. All results were consistent with the expected vision degradation caused by natural opacification.
Exploratory visualization of biological networks
Understanding the complex relationships between biological entities has a great significance in drug discovery and development. There has been a substantial investment of research effort for this purpose. However, attempts for drug discovery and development are time consuming and costly. Thus, researchers seek computational approaches to reduce the time and cost and minimize the risk of adverse events of clinical experiments. In recent years, advancements in biomedical research amplify the vast accumulation of biological data. Consequently, the known relationship and attribute information of biological entities can be used to model biological relationships in the manner of biological networks to understand the complex relationship between biological entities along with revealing latent relationships that can excel the discovery of potential therapeutic treatments. In this thesis, we introduce a dimensionality reduction-based framework, named I-UMAP, to model complex biological relationships. The proposed framework accurately models the biological networks, in our case drug--target interaction networks, to be used in exploratory data analysis to comprehend the essential biological relationships. Since the introduced framework exploits the known relationship information along with entity properties, the crucial interactions between biological entities can also be unveiled. Therefore, this task can be formulated as a link prediction problem amongst biological entities. We introduced a novel approach to benefit from both the known interaction information and entity features. In order to enhance the capacity of the base algorithm UMAP, we modified the UMAP algorithm to improve the optimization performance. To test the efficacy of our algorithm, we conducted experiments on drug--target interaction networks and drug--disease interaction networks. The results of the conducted experiments demonstrated that I-UMAP surpasses the performance of UMAP algorithm and could be beneficial to explore and unveil biological relationships.
Biyobozunur substrat modellenmesi için mikrofabrikasyon stratejileri
Replacing the non-degradable materials with the biodegradable ones is a crucial strategy for removing environmental waste and boosting eco-friendly practices. In this sense, in the recent years, both in the medicine and industry, non-degradable materials are being replaced with their degradable alternatives. Cell culturing applications, drug delivery applications, and fabrication of other implantable medical devices are some examples where the biodegradable alternative materials are highly desired. The processability of the biodegradable substrates significantly depend on the microfabrication method that is chosen to process it. For this reason, in order to make use of the biodegradable materials, providing a detailed examination of the microfabrication strategies for the patterning of biodegradable substrates is very critical. This thesis investigates the conventional and unconventional fabrication methods to craft microstructures on biodegradable PLA substrate. As the PLA is a very sensitive biodegradable material, the use of conventional microfabrication methods such as photolithography, microstamping, and laser ablation is very limited in the laboratory as well as in the industry. In this work, stencil lithography using DRIE-based Si-stencils for both PLA etching and material deposition simultaneously are utilized. In addition to separately etching and depositing metals on substrates, a molybdenum electrode embedded inside PLA substrate is demonstrated. While the average resistance is measured as 796.45 Ω when the electrodes are on top of PLA substrate, the average resistance is measured as 2.0297 kΩ when the electrodes are embedded inside the PLA substrate due to the roughness caused by etching. Overall, we provide a handbook to wisely select a protocol for large area and high throughput fabrication of any microstructure on PLA biodegradable substrate, which can be extended to a variety of other sensitive biodegradable materials.
Geçici yüzeylerde metal desenlendirme için DRIE tabanlı bir şablon maskesinin geliştirilmesi
Electronics with the potential to disappear or disintegrate into non-traceable remains after a stable performance have attracted significant interest. These categories of devices have been established based on the integration of conductive layers with polymeric substrates. Developing a compatible fabrication method is critical in the case of biodegradable substrates due to their delicate nature. However, lack of a simple and efficient microfabrication method in biodegradable device fabrication results in large sized, and low output in comparison with silicon-based devices. Stencil lithography (SL), which uses a perforated membrane as a reusable shadow mask to pattern metal on substrates offers a straightforward and flexible method for the fabrication of functional devices on a wide range of substrate materials. Here, a silicon-based stencil mask is fabricated by deep reactive ion etching (DRIE) technique using a 1:1 aspect ratio recipe to serve multiple purposes. The application of DRIE-based silicon stencil metal patterning is investigated by metal patterning (molybdenum and gold) on different substrates such as polylactic acid (PLA), polyglycerol sebacate (PGS), polyimide and polydimethylsiloxane (PDMS). PLA and PGS are widely used biodegradable materials with flexibility and stretchability features. The resistance levels of the resistor patterned on PLA and polyimide are 796.63 ± 0.14 Ω and 658 ± 0.03 Ω, respectively, which are very close to the theoretical calculations. Polyimide and PDMS are common nondegradable substrates with flexibility and stretchability properties, respectively. As another application, the silicon-based stencil mask application is demonstrated for etching the PLA substrate. The degradation behavior of the biodegradable samples is investigated in a phosphate-buffered saline (PBS) solution. The work presented here provides a facile and resist-free fabrication method using DRIE-based silicon stencil for metal patterning on the transient substrates.
Development of a modular pulmonary resuscitation device for chronic and acute respiratory support
Noninvasive ventilation (NIV) and invasive ventilation are two distinct approaches to managing respiratory failure and supporting individuals with impaired breathing. These techniques are crucial in critical care medicine and respiratory therapy, offering life-saving interventions for various pulmonary disorders. Noninvasive ventilation represents a method of respiratory support that aids patients without requiring invasive procedures such as endotracheal intubation. It typically involves the use of a noninvasive ventilator or positive airway pressure devices to deliver air or oxygen through a mask or interface, aiding patients in maintaining adequate oxygenation and carbon dioxide removal. NIV has emerged as a preferred choice in various clinical scenarios, including chronic obstructive pulmonary disease (COPD) exacerbations, acute respiratory failure, congestive heart failure, and sleep-related breathing disorders. This approach offers several distinct advantages, such as reduced risk of ventilator-associated pneumonia, improved patient comfort, and the possibility of patient self-management, making it an increasingly valuable tool in respiratory medicine. The emergence of the COVID-19 pandemic in 2020 prompted the creation of numerous affordable, open-source, or readily constructed ventilators for urgent deployment. However, most of the proposed setups constituted of either automation of a hand-operated resuscitator called Bag Valve Mask (BVM), which is limited in its ability for pressure and volume control, or the development of pressurized valve-based mechanisms that require a constant high-pressure input source, making them redundant in scenarios where pressurized air/oxygen source is not available. Furthermore, these solutions are generally catered towards invasive and intubated mechanical ventilation techniques. Turbine-based positive pressure ventilators bridge the gap between portability and advanced therapy modes for pulmonary therapy via non-invasive ventilation. The existing body of literature exhibits a notable paucity of comprehensive examinations concerning the conception, evaluation, and viability of turbine-based non-invasive ventilators as an economically efficient and readily deployable platform for respiratory support. This deficiency in research extends to the exploration of their potential applications in contexts extending beyond emergency situations, particularly in the domain of home care ventilation. This thesis delves into examining and evaluating the creation of a modular respiratory system that can provide continuous positive pressure and Bilevel positive pressure therapy. In the first phase of this research study, a high-pressure turbine-based positive-pressure support, non-invasive ventilator design is proposed. The developed hardware can deliver multi-mode respiratory therapy, namely pressure support and volume-assured pressure support ventilation. The novel modular device works as a non-invasive respiratory support device with novel algorithms developed to maximize patient machine synchronization and robust closed-loop control strategy for pressure therapy during varying pulmonary compliance. In the second part of this research, a novel real-time wireless sensory module technique is presented for advanced respiratory monitoring and control during non-invasive ventilation. The proposed techniques focus on improving the current standards of monitoring and therapy in continuous positive pressure systems utilizing single-limb circuits with passive leak ports. Implementing the proposed wireless pressure and flow monitoring, in conjunction with the developed modular respiratory device, yields enhancements in the device's responsiveness in detecting distinct patient respiratory phases. Furthermore, this setup effectively alleviates the necessity for computational modeling of dynamic leakages, consequently facilitating the precise monitoring of inspiratory and expiratory tidal volumes in Non-Invasive Ventilation (NIV). Notably, these capabilities significantly advance compared to conventional homecare ventilatory support utilizing single-limb passive leak circuits. In the third part of this research, real-time assessment for pulmonary mechanics is performed via Machine learning techniques from data acquired in real-time during non-invasive pressure therapy mode. The pulmonary mechanics are key monitoring parameters for ensuring correct therapy mode and therapy pressure or volume levels are provided for patient care. To date, for pulmonary mechanic measurement, an inhalation pause maneuver is adapted. This maneuver is only possible during invasive mechanical ventilation, where patient-derived breathing is absent, and the total breathing is controlled via the ventilator. The absence of an inhalation pause maneuver or any active spirometry during non-invasive ventilation makes monitoring pulmonary mechanics extremely challenging. Thus we present a novel framework for the development of machine learning techniques that can predict pulmonary mechanics like compliance and resistance with an overall accuracy above 95% with and without system leakages, leading to a novel digital framework that allows for lung mechanics monitoring without clinical intervention and can help save ventilator induced lung injuries.
Enhancing the performance of a coagulometer through optimization of microfluidic cartridge and fiber optic-based optomechanical systems
More than 800 million clotting tests are performed each year in hospitals and clinical laboratories for emergencies, surgical operations, and periodic monitoring of patients. Monitoring of adequate anticoagulant dosage is essential to maintain the delicate balance between bleeding and thrombosis. The primary means of monitoring the response to warfarin (VKAs) is the Prothrombin Time (PT) test and the international normalized ratio (INR) while activated partial thrombosplastin time (aPTT) is used for heparin monitoring. Current clinical laboratory tests used to routinely measure blood coagulation still lack in rapidity and simplicity. Whole-blood Point-of-Care (PoC) coagulation devices that respond to the exact needs of both clinicians and patients are still emerging in the field. Portable PoC and self- care PT/INR monitoring devices are gaining in popularity as they provide crucial advantages over traditional laboratory methods such as ease of use, instant results, rapid turnaround for timely anticoagulant dose adjustment and improved patient convenience by removing the need for routine hospital/laboratory visits and venipunctures. Moreover, PoC devices are using whole capillary blood usually from a finger prick while conventional laboratory methods utilize centrifuged plasma obtained from citrated venous blood. This thesis presents several optimization activities that was performed on the disposable cartridge unit of an opto-mechanical-based Point-of-care and Self-care coagulometer. This study demonstrates several design optimization and validation activities undertaken during the product development stage in order to move the initial cartridge design into a commercializable product. Thus, this work focused of increasing the manufacturability and usability of the previous cartridge design developed by our group in terms of passive capillary flow/Microfluidics, biochemical functionalization, optical fiber assembly, and reagent optimization. Furthermore, the final cartridge design was used to conduct a proof-of-concept study in the topic of heparin monitoring and aPTT measurement on control plasma and blood samples, suggesting a reliable and rapid testing as a PoC device. A preclinical trial was conducted with an n=42 sample size to assess the correlation between our device and the standard hospital method, further validating its efficacy and potential for clinical use.
The development of the 3D micropatterned ECM (extracellular matrix) models of glioma-astrocyte co-culture: Investigating glioma migration and astrocyte reactivity
Glioblastoma multiforme (GBM) is the most fatal type of primary malignant brain tumors, characterized by aggressive infiltration into brain tissue. GBM migration is a complex process affected by several factors, including the bilateral communication between the GBM tumor and its microenvironment (TME). Astrocytes, the star-shaped stromal components of the GBM TME, account for half of the brain cells; however, their exact role within GBM invasiveness remains not fully understood. The utilization of scaffold-based 3D cell culture platforms has emerged as a promising strategy to mimic the complexity of the GBM TME. Among them, hydrogels with tunable biochemical and mechanical properties are ideal for replicating the low-stiffness and well-hydrated extracellular matrix (ECM) of the brain. The photocrosslinkable, semi-synthetic hydrogel, gelatin methacrylate (GelMA) offers advantages of cell-responsiveness and biodegradability, simultaneously providing a fine level of control over its mechanical properties, including matrix stiffness and porosity. In this thesis, it was aimed to establish an in vitro 3D co-culture model of the GBM TME. To accomplish this goal, a two-step photolithography technique with photomasks was employed to surround high-stiffness U87 GBM cells encapsulated in GelMA microspheres, resembling glioma tumors, by lower-stiffness GelMA matrices, mimicking the healthy brain parenchyma. This technique facilitated the establishment of two distinct astrocyte-glioma co-culture configurations, demonstrating the versatility of the proposed microfabrication technique in precisely localizing various cell types. The quantitative analysis of time-lapse confocal microscopy images revealed the differential impact of the immortalized normal human astrocyte (I-NHA) co-culture configuration on GBM migration. Encapsulating I-NHA cells in vicinity to U87 GBM cells resulted in extensive invasion of the surrounding GelMA matrix by GBM cells. In contrast, surrounding U87 GBM microspheres with an astrocyte-dispersed matrix led to the establishment of the astrocytic network, which inhibited the tumor cell migration. To further validate the physiological relevance of the microfabricated platform, we performed the immunofluorescent staining and qPCR analysis of proteins and genes related to GBM migration and malignancy as well as astrocyte reactivity. The immunocytochemical staining confirmed the upregulation of GFAP expression by interconnected astrocytic networks around U87 microspheres, suggesting the reactive transformation of astrocytes and the formation of the glial scar in the presence of GBM cells. Additionally, culturing U87 cells in the 3D environment of GelMA microspheres resulted in the upregulation of genes linked to GBM invasiveness, including MMP family proteases (MMP-2, MMP-9, MMP-14), hypoxia-related factors (VEGF, HIF-1α), and epithelial-to-mesenchymal transition (EMT) markers (CD44, FN1, TGF-β). In conclusion, this thesis presents a 3D micropatterned co-culture model of the GBM TME, offering a novel biomimetic in vitro tool for advancing our understanding of GBM migration and the intricate dynamics within the GBM TME.
Electronics system integration and characterization of electronic skin for prosthetic applications
Upper limb amputation significantly disrupts tactile perception, having a crucial impact on daily activities. For attaining a prosthetic device that closely mimics natural functioning, it is crucial to provide users with enhanced sensory experiences during interactions with objects. Through sensory feedback, the ideal upper limb prosthesis must provide real-time mirroring of the user's natural experiences. Current prostheses face challenges in delivering substantial tactile feedback due to their limited sensory capabilities. Here, inspired by the sensory characteristics of the skin, we describe a micro-fabricated and multiplexed electronic skin that is combined with a suite of actuators for sensory feedback capabilities, and employed for upper limb amputation. The set of piezoelectric-capacitive sensors can identify static pressure, temperature, vibration, and texture, while the incorporated actuators offer instantaneous feedback through skin stimulation. The fabricated sensor array has a flexible structure and a compact design of two pixels inside a 1 cm2 footprint. This array of sensors is capable of detecting a wide range of pressure (0.5-10 kPa), temperature (22-60 °C), vibration (35-100 Hz), and texture (2.5-45 Hz) which are the most important tactile sensations of the human skin. The electronic skin is affixed to a prosthetic finger, while the actuators are positioned on the wrists of the human volunteers. Human participants participated in feasibility tests of the system, and its performance was quantitatively evaluated using statistical methods. The incorporation of multiplexed sensors and actuators introduces novel prospects for delivering improved tactile feedback and enhancing the quality of life for individuals with upper limb amputation.
Glio-SERS: Artificial intelligence and surface enhanced raman spectroscopy driven liquid biopsy method for brain tumor classification
Glioblastoma (GB), the most aggressive adult brain tumor, requires invasive procedures such as biopsy or surgical intervention, along with sophisticated laboratory settings and prolonged, costly molecular testing for accurate diagnosis. Nearly all patients with GB experience tumor regrowth within two years after primary surgery. The current management of gliomas relies on diagnostic imaging, which lacks the high sensitivity and specificity needed to evaluate recurrence after primary treatment. Implementing liquid biopsy in gliomas is essential for early diagnosis, detecting residual disease after surgery, and assessing disease status post-treatment. With an average survival rate of just 14 months, there is an urgent need for rapid, accurate, cost-effective, and minimally invasive diagnostic strategies. This study introduces a transformative diagnostic paradigm—a liquid biopsy approach that merges Surface-Enhanced Raman Spectroscopy (SERS) analysis of exosomes with artificial intelligence (AI). In a prospective study, we evaluated the efficacy of this SERS and AI-based liquid biopsy analysis for GB detection. We collected 20 glioblastoma, 24 meningioma (MNG) as the most frequent benign tumor control, and 30 healthy control (HC) plasma samples under informed consent and IRB approval. SERS was employed to analyze the isolated plasma exosomes, generating spectral data on molecular signatures indicative of each condition. Deep learning algorithms were integrated into the analysis pipeline to facilitate rapid and accurate differentiation between GB, MNG, and HC plasma exosome SERS signatures. Our approach achieved a remarkable 87\% prediction accuracy in distinguishing GB exosomal signatures from those of MNG and HC individuals. This result signifies a substantial advancement in the precision and speed of GB diagnostics compared to traditional methods. This pioneering liquid biopsy technique emerges as a front-line solution for GB detection, differentiation, and monitoring. The ongoing integration of an expansive library of tumor signatures signifies a significant leap forward in analytical technologies tailored for neuro-oncology. Our study demonstrates not only the technological superiority of our approach but also its potential to revolutionize GB detection and improve patient care once it is clinically validated with a larger cohort.
Hemodynamic assessment of self-expandable pulmonary valve in treating surgically repaired tetralogy of Fallot using 3D printed models
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease, accounting for 7% of all live births with congenital heart defects. TOF is characterized by four primary anomalies: a ventricular septal defect (VSD), an overriding aorta, right ventricular hypertrophy, and right ventricular outflow tract obstruction (RVOTO). The standard surgical intervention, typically performed within the first year of life, involves VSD closure and relief of RVOTO. Despite the initial success of these surgeries, long-term complications such as right heart failure, arrhythmias, and sudden cardiac death frequently occur. These complications are often attributed to pulmonary regurgitation (PR), which results from the transannular patch used during repair, leading to right ventricular (RV) enlargement and dysfunction over time. Pulmonary valve replacement (PVR) has become essential for managing PR and restoring RV function. Traditional options, including homografts, xenografts, and various bioprosthetic valves, are associated with limited durability and potential for reoperation due to calcification, degeneration, and somatic outgrowth, particularly in younger patients. These limitations have prompted the development of less invasive alternatives, such as percutaneous pulmonary valve implantation (PPVI), which offers the advantages of reduced procedural risk and shorter recovery times. This dissertation focuses on the hemodynamic assessment of self-expandable pulmonary valves, specifically the Pulsta® valve , in treating surgically repaired TOF. The Pulsta® valve, a significant advancement in the field, consists of a nitinol wire stent frame and decellularized porcine pericardium leaflets designed for deployment in the native RVOT without a rigid supporting frame, allowing for a more flexible adaptation to the patient's anatomy. The A key innovation in this study is the utilization of 3D-printed models to simulate patient-specific anatomies. These models, a testament to the rapid advancements in technology, enable precise pre-procedural planning and optimization of valve selection and implantation techniques. By creating accurate replicas of the patient's heart, 3D printing technology allows for detailed assessment of the valves' anatomical fit and functional performance under various physiological conditions. Hemodynamic assessments include evaluating pressure gradients, valve function, and the absence of obstruction or regurgitation, which are crucial for determining the success and durability of the implanted valves. This approach, with its precision and risk reduction, provides a sense of security and confidence in the procedure, enhancing the overall quality of care. The research aims to provide comprehensive insights into the long-term outcomes of self-expandable valves in the native RVOT. By leveraging advanced imaging and 3D printing technologies, this study significantly enhances our understanding of TOF management, potentially reducing the need for repeated interventions and improving patient outcomes. The findings contribute significantly to biomedical engineering and bioinformatics, offering promising directions for future research and clinical practice in congenital heart disease treatment and, ultimately, improving the quality of life for TOF patients.
Development of carbon quantum dots for the selective and sensitive detection of nitrite ions
Nitrite ion is used as a preservative in food and beverages and is also a common pollutant emerging from industrial processes. The concentration of nitrite requires strict control due to its toxicity and reactivity. It is also an indicator of infections in the human body. Detection of nitrite concentration via effective, cheap, and sustainable methods will help regulation of industrial uses and early diagnosis of diseases mostly related with the respiratory system. Carbon dots are a relatively new class of luminescent nanoparticles and are highly promising in sensing applications due to their tunable, functional group-rich surface and fluorescence properties. The lack of heavy metals, ease of production and biocompatibility, the lack of surface capping agents make the luminescence of carbon dots highly sensitive to the surrounding media and favorable for sensing applications. The development of carbon dots from various carbon sources including small molecules and polyolefins has been studied to produce stable, reproducible, low-cost carbon dots with high quantum yield and various emission profiles. Red luminescent carbon dots were developed for highly selective and sensitive nitrite sensing with 0.01 ppm limit of detection (LOD). From the emergence of plastics in the early 20th century, plastics replaced many materials due to cost, light weight, durability, etc. Today, humanity faces the problem of plastic pollution as a result of the large volume of production but insufficient recycling. Chemical stability and corrosion resistance of plastics especially polyolefins like polyethylene (PE) and polypropylene (PP), make the recycle processes highly expensive and inefficient. Conversion of these polyolefins to the value-added carbon nanoparticles proposes an efficient way to handle plastic pollution. Upcycling of polyolefins to luminescent carbon dots with high quantum and conversion efficiency is demonstrated in this thesis as an alternative to polymer recycling.
Development of Istanbul heart version 2
Heart Failure (HF) continues to be a leading cause of death due to the shortage of donors for transplantation. This shortage has led to the development of several alternative solutions/therapies. Mechanical Circulatory Support Devices (MCSD) are one possible solution that has been proposed. Left Ventricular Assist Device (LVAD) is one of the most common MCSD available. LVADs are generally used as a bridge-to-transplant, bridge-to-recovery, or destination therapy for HF patients. Of the many LVAD design considerations, ensuring blood compatibility and hemolysis prevention is of paramount importance. This study aims to develop a small and compact version of the Istanbul Heart (iHeart). Computational Fluid Dynamics (CFD) has been employed in reducing the size and optimizing the impeller geometry while maintaining the required performance attributes. The LVAD impeller diameter is reduced to 30 mm while wrap angles are varied to minimize the hemolysis index and to deliver a 5 L/min flow rate at 100 mm-Hg. In-silico tests are performed to find the best impeller geometry achieving the set conditions. An experimental study was performed to validate the simulations. The experiments measured the hydraulic performance in terms of pressure and flow rate as well as the hemolytic performance in terms of hematocrit and plasma-free hemoglobin. Finally, an initial in-vivo study is conducted for the selected LVAD design. Two adult sheep weighing around 50 kg have been used to evaluate the anatomical fitting, biocompatibility, and performance of the LVAD in the short term.
Wireless wearable reader platform for continuous healthcare monitoring with power harvesting
Wearable and implantable healthcare monitoring devices have become essential in modern medicine due to their ability to provide reliable and real-time data on individuals' health status. These devices facilitate continuous monitoring, early intervention, and personalized care, leading to improved patient outcomes and reduced strain on healthcare systems. The advanced capabilities of wearable and implantable devices have made it possible to design and fabricate platforms that can simultaneously measure and report critical health-related metrics within the human body. In this thesis, we will demonstrate our proposed approaches and developed platforms for healthcare monitoring. As a first non-invasive wearable device, we developed a fully integrated sensing system capable of detecting low glucose concentrations, acquiring heartrate variability (HRV) data, and sensing temperature from human skin. The system can be easily attached to the skin, offering direct read-out and wireless signal transmission, with extended battery life through continuous RF-based charging. The platform can measure glucose concentration using a microfluidic sensory patch with an embedded screen-printed glucose sensor. Furthermore, the device uses a photoplethysmography module and temperature sensor to monitor HRV and temperature values and transmitting them to the user's smart devices. In another effort, we proposed and developed a wearable platform for continuous and simultaneous monitoring of the different biomarkers. We tested the device by measuring sodium, potassium, and pH levels in real-time and transmit them to the user's smart devices over Bluetooth. Moreover, this platform features the NFC power harvesting allowing for long-term monitoring by charging a rechargeable battery. The fabricated platform can be used as a minimally invasive health monitoring device by integrating hollow microneedles patch for interstitial fluid extraction. This approach provides further opportunities to acquire data from multiple biomarkers related to various diseases and diagnostics, offering a highly accurate approach to health monitoring. Taking this a step further, we proposed the design and fabrication of a standalone wireless system capable of capturing frequency shifts in fully passive implantable or wearable sensors. Our approach addresses invasive measurement issues by replacing traditional physical interconnections and power-hungry systems with a wireless signal reader and power harvesting platform. The device's power harvesting capability allows continuous long-term measurement without the need for frequent battery replacements. The fabricated wireless reader continuously measures and calculates frequency shifts induced on the passive sensor by the reader coil. This device can be used with various passive LCR sensors to continuously analyze critical health-related signals and biomarkers, making it a potential candidate for real-time physiological and clinical investigations as a next-generation wearable healthcare monitoring system.
Kompakt bir sol ventriküler destek cihazının geliştirilmesi: İstanbul Kalp versiyon II
The shortage of heart donors has led to the development of mechanical circulatory support devices for patients suffering from heart failure. Most of these devices are bulky and require adequate space in the chest cavity for implantation, mainly left ventricular assist devices. However, patients with small chest cavities face challenges during implantation. Therefore, it is crucial to develop a compact version of the left ventricular assist device that is smaller yet capable of providing sufficient flow rate, head pressure, and biocompatibility. In this research study, a novel compact left ventricular assist device is designed and developed for patients with small chest cavities. Firstly, the significance of the research is presented, including the statistical information regarding heart-failing patients and the number of available donors worldwide. Subsequently, the main aim behind this research is elaborated. Then, a brief literature review of the human cardiovascular system is reported, and the reasons that led to heart failure are discussed. Following this, mechanical circulatory support devices are presented, which are used to support the failing heart. Then, a rationale for the various kinds of these devices is provided, followed by a discussion of the evolution of the blood pump generations. In the third part of this thesis, the design and development of the ventricular device is outlined, which elaborates the design process. A prototype model of the blood pump was manufactured based on the simulation results. These prototyped models of the blood pumps are then extensively tested in vivo and in vitro to verify hydraulic and hemolytic efficiency. The results of both device evaluations are on par with those of commercially available devices. In the future, acute tests can provide an in-depth analysis of the developed prototype of short-term assessment. Later, a mock circulatory loop was designed and developed to test the working performance of the developed prototype device in vitro scenario.
Hollow microneedle-based sampling and sensing of dermal interstitial fluid
Microneedle-based biosensing platforms have emerged as a promising alternative for blood-based health monitoring devices. Microneedles (MNs) can access the dermal interstitial fluid (ISF) in a painless and blood-free manner, enabling the detection of a wide range of biomarkers. Although in-skin biomarker monitoring using functionalized solid MNs remains attractive due to the challenging task of ISF sampling, there is growing attention toward the integration of biosensors into ISF sampling platforms. ISF sampling can be followed by measuring the biomarker level using the integrated biosensors. Recently, microfluidic-based biosensing devices have been incorporated with hollow MNs (HMNs) to enable the detection of target biomarkers in the collected dermal ISF. In this thesis, we report the development of HMN-based platforms integrated with microfluidic ISF collection chambers to provide the necessary contact between the sampled ISF and biosensors. Chapter one establishes a concise overview of recent advancements in the manufacturing of various HMNs and their integration into diverse biosensing devices. In chapter two, we demonstrate the integration of laser-drilled HMNs with a touch-activated vacuum source to enable continuous sampling of ISF with subsequent electrochemical sensing of glucose and pH levels. The wearable vacuum system leverages the self-recovery feature of the utilized elastomer to create the necessary negative pressure for ISF sampling. The developed touch-activated system shows ISF extraction rate of approximately 17 μL h-1 in vivo. We demonstrate the capacity of the developed platform in continuous health monitoring by measuring the glucose and pH levels in animal models. Chapter three presents our efforts in developing a hydrophilic 3D-printed HMN-based platform for measuring the pH and urea levels in the collected ISF using colorimetric techniques. Multichannel MNs are fabricated using high-precision projection micro stereolithography technology, followed by deposition of an oxide layer using plasma enhanced chemical vapor deposition (PECVD) to enhance the wettability of MNs for effective ISF collection. The oxide layer results in a significant decrease in water contact angle of the 3D-printed films from about 72° to 9°, rendering them superhydrophilic. The enhanced wettability of the surfaces leads to an improved liquid uptake capability of the MNs from agarose hydrogel and rat skin samples. We demonstrate the applicability of the developed approach by ex vivo colorimetric sensing of pH and urea. Overall, the devices developed offer promising advancements in technology and exhibit great promise for enhancing biomedical sensing and diagnostic applications.
AI-Augmented 3dp microfluidic bio-reaction system for point-of-care detection of mpox via LAMP-on-a-chip
Microfluidic devices hold enormous potential for high-throughput, low-cost, and point-of-care (PoC) biological assays, yet current fabrication and control strategies limit their scalability and automation. In this thesis, we first demonstrate that digital light processing (DLP) 3D printing provides a rapid and economical alternative to conventional soft lithography by reproducing a complex organ-on-chip. We then integrate finite element modeling (FEM) simulations with machine learning (ML) tools to create a user-friendly interface for designing single-phase flow circuits that achieve target flow rates with high accuracy. Next, we introduce programmable 3D microfluidic reaction reservoirs that utilize pressure-dependent two-phase (water/air) fluid control in hydrophobic channels. Adjusting the inlet pressure allows fluid to be temporarily retained in these reservoirs for precisely timed reactions, and then released into following reservoirs, facilitating automated consecutive or parallel assays. To further expand accessibility, a low-cost, portable pressure pump was developed to eliminate reliance on bulky, expensive equipment. The utility of the integrated approach is demonstrated through a PoC Loop-mediated Isothermal Amplification (LAMP)-on-chip assay targeting monkeypox markers. The sample fluid, heated to 65°C for 30 minutes, interacts with pre-immobilized LAMP primers within the reservoir, producing a distinct colorimetric shift that confirms the presence of the pathogen. The automated control of fluid handling and reaction timing proved the system's potential for PoC diagnostics. Collectively, the presented methodologies pave the way for more accessible, precise, and autonomous PoC bioassays.
Fabrication and characterization of solution-gated graphene field-effect transistors and graphene hall sensors for developing microfluidic molecular communication receivers
Molecular Communication (MC) is a bio-inspired communication paradigm that uses chemical signals to transmit information between spatially separated entities. While significant research has been conducted on the theoretical aspects of MC, there remains a notable gap in developing practical systems that can transition these concepts into real-world applications. The absence of established testbeds at the micro- and nanoscale often leads researchers to rely on simplified assumptions regarding channel conditions and transceiver designs. Furthermore, MC presents unique challenges due to its highly complex, nonlinear, and time-varying channel properties, which conventional ICT tools cannot adequately address. As a result, many existing MC methods, largely adapted from traditional electromagnetic communication models, remain unvalidated without practical testbeds. To bridge this gap, it is essential to develop practical MC systems with nanoscale MC receivers that can serve as testbeds for advancing realistic MC methods and Internet of Bio-Nano Things (IoBNT) applications. In this context, micro/nanoscale field-effect transistor (FET)-based biosensors and Hall effect sensors emerge as promising architectures for practical MC receivers due to their ability to selectively detect a wide range of molecules that can be used to encode information. FET-based sensors detect charged information molecules, such as nucleotides, through ligand-receptor interactions that modulate the FET channel conductivity. In contrast, Hall effect sensors are designed to detect magnetic nanoparticles (MNPs), which alter the local magnetic field, inducing measurable voltage modulation based on the Hall effect. Both sensor architectures enable continuous, label-free, and selective molecular detection, making them well-suited for integration into MC systems as receivers. Graphene, with its exceptional electrical properties, stands out among nanomaterials used for FET-based biosensors and Hall effect sensors. In light of this, in this thesis, I report the design and fabrication processes of MC receivers based on graphene FET-based DNA sensors and graphene Hall effect sensors. Key challenges addressed include precise graphene transfer, formation of high-quality metal electrodes, deposition of effective dielectric layers, and integration with microfluidic channels, along with specific challenges related to MC receiver applications beyond conventional sensing. Through optical and electrical characterization methods, I evaluate the performance and quality of both sensors, confirming their potential as sensitive and reliable MC receivers. As such, this thesis lays the foundation for the development of practical MC systems and contributes to advancing realistic MC methods and IoBNT applications.
Translational biomaterials and engineering approaches forcorneal regeneration: targeting stromal stabilization andlimbal stem cell deficiency
Cornea is a transparent and avascular tissue essential for maintaining clear vision. However, corneal ectatic disorders, such as keratoconus, lead to progressive thinning and biomechanical weakening, causing the cornea to lose its regular shape. While riboflavin/ultraviolet-A (UVA) corneal crosslinking (CXL) is widely used to enhance corneal rigidity in clinics, it presents challenges such as cytotoxicity, patient discomfort, and treatment failure in some cases. In addition to biomechanical instability, damage to the limbal region can lead to limbal stem cell deficiency (LSCD), a condition characterized by the loss or dysfunction of limbal stem cells responsible for regenerating the corneal epithelium. LSCD results in impaired wound healing, chronic inflammation, neovascularization, and vision loss, making stem cell-based therapies crucial for corneal surface restoration. This research presents two innovative therapeutic strategies: (1) Ruthenium-blue light mediated CXL as a safer and more effective alternative to Riboflavin-UVA based CXL for corneal stabilization, and (2) FasL-conjugated GelMA nanogels incorporated into human limbal stem cell heterospheroids to enhance transplantation outcomes by inducing apoptosis in immune cells and thereby reducing immune rejection. To overcome the limitations associated with clinical treatments, the first part of this thesis explores an alternative CXL approach utilizing tris(bipyridine)ruthenium(II) ([Ru(bpy)₃]²⁺) and sodium persulfate (SPS) with blue light (430 nm) to induce collagen crosslinking via dityrosine bond formation. The study evaluates the safety and efficacy of ruthenium mediated CXL in ex vivo bovine corneas and in vivo Wistar albino rat models, comparing its structural and histological effects with conventional riboflavin/UVA CXL. The findings indicate that ruthenium mediated CXL effectively enhances corneal stiffness while minimizing UV-induced cellular damage, presenting a promising clinical alternative for keratoconus treatment. The second part of this thesis addresses limbal stem cell deficiency (LSCD). Current limbal stem cell transplantation methods are hindered by immune rejection, necessitating systemic immunosuppression. To mitigate this issue, we propose a novel strategy leveraging the Fas/Fas ligand (FasL) pathway for localized immune modulation. By functionalizing gelatin methacryloyl (GelMA) nanogels with FasL, we developed an immune-protective biomaterial to enhance limbal stem cell survival post-transplantation. These advancements contribute to the development of clinically viable therapies for corneal disorders, improving treatment outcomes for keratoconus and LSCD.
A smart magnetic sensing system for non-destructive material property characterization
Non-destructive testing (NDT) and evaluation methods offer fast and online alternatives to other traditional techniques. This thesis focuses on magnetic techniques such as Magnetic Barkhausen Noise (MBN) and Eddy Current (EC), which have been analyzed and applied for the construction of a novel magnetic sensor. The first part focuses on thickness estimation with a physics based analytical approach: The EC problem is solved analytically to create voltage vs. thickness plots. Namely, setup and material properties are provided to an optimized algorithm for the estimation of the pick-up voltage in the presence of a conductive sheet with varying thicknesses. The voltage signal of the pick-up winding is then measured and processed. The signal processing step involves the extraction of the dominant frequency by sine and cosine projection and reconstructing it by multiplying the amplitude with a fixed-phase sine wave resulting in the complete elimination of background noise and possible phase shifts. The signal is then averaged over 10 measurements and the amplitude is mapped to the analytical graphs enabling the estimation of thickness. The second part details the assessment of material properties by MBN analysis. Specifically, the Barkhausen effect is employed to detect superficial atmospheric rust in steel sheets. The MBN signals each composed of 4 bursts per window are sampled with an analog oscilloscope, and inserted to the signal conditioning program. A novel signal processing algorithm and CNN network with a low computational cost is proposed for accurate and fast rust classification. Experiments performed on DC04 cold-rolled uncoated steel sheets validate the results of the magnetic sensor. The tests demonstrate that the proposed sensor is a suitable alternative where continuous material property monitoring is needed. In addition to their various applications in industrial sectors, these types of sensors hold significant potential for future use in detecting material loss, assessing surface degradation, and evaluating stress in biomedical implants.
Synthesis of cadmium-based and cadmium-free colloidal nanocrystals for efficient lighting, display and biomedical applications
Colloidal semiconductor nanocrystals have gained significant interest in recent years as promising materials for next-generation optoelectronic and biomedical technologies, owing to their tunable optical properties, high photoluminescence efficiency, and compatibility with solution-processable synthesis routes. Their potential in solid-state lighting, display technologies, and neural interfaces continues to expand as performance demands increase. This dissertation presents a detailed investigation into the synthesis, structural tuning, and integration of both cadmium-based and cadmium-free colloidal nanocrystals. Alongside application-focused studies, it also introduces the development of a new core/shell nanocrystal system, investigated primarily from a materials chemistry perspective. In the first part of this thesis, cadmium-based quantum dots (QDs) were developed with optimized optical properties for high-performance white light-emitting diodes (WLEDs). The ZnCdSe/ZnSe core/shell QDs, synthesized via low-temperature nucleation followed by high-temperature shell growth, exhibited photoluminescence quantum yields (PLQYs) up to 94%. When integrated into a liquid-type LED configuration, the total cadmium content in the final device remained below 100 ppm, in compliance with current RoHS regulations. This integration led to luminous efficiency values exceeding 170 lm/W, and simulations suggested that efficiencies above 230 lm/W could be achieved using ultra-efficient blue LED pumps. In the second part of this thesis, highly emissive green CdZnSeS/ZnS and red-emitting giant CdSe/CdS QDs were synthesized to enhance display backlighting performance, yielding near-unity PLQYs and narrow emission bandwidths. When incorporated into a liquid matrix over blue LEDs, these QDs enabled devices with external quantum efficiencies (EQEs) reaching up to 39.8% and a color gamut coverage of 133.3% NTSC. These results indicate that QD-based LEDs can outperform conventional color enhancement films while significantly reducing the amount of material required. In the third part of this thesis, further improvements were achieved by tailoring the morphology of nanocrystals. A dot-to-rod transition in CdSe/CdS QDs introduced a large Stokes shift (~780 meV), effectively minimizing reabsorption losses. When combined with green-emitting ZnCdSe/ZnSe QDs, the resulting white LED devices achieved an EQE of 42.9%, representing more than a 10% improvement compared to systems utilizing QDs alone. In the fourth part of this thesis, cadmium-free AgBiS2 nanocrystals were developed as an environmentally friendly alternative to address sustainability concerns. For the first time, a novel wet-chemical method was established to grow ZnS shells on high-quality AgBiS2 cores, resulting in the formation of AgBiS2/ZnS core/shell nanocrystals. This approach led to the first reported photoluminescence from AgBiS2 nanocrystals, with emission centered at 764 nm and a PLQY of 15.3%. Their strong near-infrared (NIR) absorption and composition of earth-abundant, non-toxic elements make these nanocrystals promising candidates for future applications in lighting, bioimaging, and NIR optoelectronics. In the fifth and final part of this thesis, AgBiS2 nanocrystals were implemented in neural interface devices. A thin (24 nm) nanocrystal film generated a stable photocurrent of 2.3 mA·cm−2 and achieved charge injection levels exceeding 10 μC·cm−2 in artificial cerebrospinal fluid. No cytotoxicity was observed in neuronal cultures, and patch-clamp recordings confirmed reliable activation of hippocampal neurons under biologically safe near-infrared (NIR) light conditions. The device also exhibited a projected operational lifetime of over 12 years, demonstrating its strong potential for future use in minimally invasive retinal prosthetic systems. In summary, this thesis presents useful findings and developments in colloidal nanocrystal research, helping to build a solid base for sustainable and efficient materials in future lighting, display, and neural technologies.
Reduced order digital twins of cardiovascular devices and complex congenital diseases
Almost 1% of neonates are born each year with clinically significant congenital heart disease (CHD), making it the most prevalent birth defect worldwide. Among these, single ventricle (SV) malformations and severe right heart obstructions are among the most challenging, often requiring complex, multi-stage surgical reconstruction or long-term mechanical circulatory support (MCS). The management of such conditions is complicated by patient-specific anatomical variability and the lack of large clinical datasets, which limits the ability to generalize treatment protocols. In recent years, physics-based computational modeling has emerged as a promising tool to support personalized decision-making in both surgical planning and device design. This thesis explores such approaches, combining cardiovascular simulations, virtual patient modeling, and mechanical support optimization to address key clinical challenges in the treatment of CHD. The work is divided into two main parts. The first part focuses on pre-operative planning for patients with pulmonary atresia and an intact ventricular septum—a rare condition characterized by a severely underdeveloped right ventricle (RV). In these cases, choosing between biventricular repair and one-and-a-half ventricle palliation is often uncertain. To assist in this decision-making, a lumped parameter cardiovascular model was developed and used to simulate virtual patient populations with varying anatomical and physiological characteristics. For each patient, both surgical strategies were evaluated computationally, assessing post-operative pressure, flow, and oxygen delivery across the circulatory system. The results revealed patterns linking RV size and function with surgical success, supporting the potential of in silico models to act as screening tools prior to clinical intervention. This personalized modeling framework can be particularly valuable in rare congenital diseases, where evidence-based guidelines are limited. The second part of the thesis shifts focus to MCS strategies for both neonates and older children with SV physiology, particularly those at risk of surgical failure or in need of transplantation. First, a modified Norwood circulation was investigated in which pulmonary blood flow is mechanically assisted using a circulatory pump. Computational simulations showed that this approach could improve systemic perfusion and oxygenation, especially in patients with compromised ventricular function, offering an alternative pathway for high-risk neonates. Building on this, a novel support concept was proposed for patients with failing Fontan circulation, where the native SV is reassigned to support venous return while a mechanical assist device maintains systemic output. This configuration was tested in various failure scenarios using a validated cardiovascular model and showed promise as a more physiological and efficient alternative to traditional dual-pump systems. Finally, the thesis presents a new framework for designing and optimizing ventricular assist devices by integrating cardiovascular modeling with pump design software. This approach allows for efficient evaluation of pump performance under realistic physiological conditions and supports the development of patient-specific device configurations that balance flow quality with safety and efficiency. Altogether, this thesis demonstrates how integrated computational modeling can support both the clinical and engineering aspects of congenital heart disease management. By creating virtual patient populations, simulating surgical and device outcomes, and optimizing circulatory configurations, the work provides a pathway toward more personalized, predictive, and effective treatment strategies for some of the most complex conditions in pediatric cardiology.
Engineering pseudoislets for type 1 diabetes: GLP-1 gene modulation, gelma nanogel immunoisolation, and endothelial support
Type 1 diabetes arises from autoimmune destruction of pancreatic 𝛽-cells. This leads to absolute insulin deficiency and persistent hyperglycaemia. Exogenous insulin remains the standard of care, non-curative, and cannot replicate the dynamic physiology of endogenous 𝛽 cells. Islet transplantation offers an alternative. However, its broader adoption is constrained by scarce high quality donors and the need for lifelong systemic immunosuppression with associated risks. These constraints motivate continued pursuit of cell replacement strategies. In this thesis, an injectable pseudoislet is a three dimensional, self-assembled spheroid of insulin producing cells by using hanging drop, providing a scaffold free architecture. As the transplanted spheroids face immune rejection, they must be shielded from immune cell attack without compromising mass transport. Macroencapsulation commonly suffers from diffusion limits, and alginate microencapsulation adds bulk. In contrast, an ultrathin conformal nanogel coating could confer immunoisolation without compromising glucose, oxygen, or insulin diffusion. This nanobarrier also facilitates direct contact and integration to the host vasculature, which can enhance engraftment and reduce foreign-body responses. In this thesis, bovine gelatin was methacrylated to obtain gelatin methacryloyl (GelMA). GelMA is a well established biomaterial that preserves gelatin's RGD adhesion motifs and MMP-degradable sites, supporting cell attachment and remodeling. It is highly cytocompatible, readily functionalized via methacrylate groups, and tunable in stiffness. Unlike bulk or macroencapsulation, GelMA nanogels can assemble via electrostatic interactions and RGD mediated adhesions as an ultrathin, conformal barrier around individual spheroids. This configuration minimizes diffusion barriers for glucose and oxygen while providing an immunoisolating shield that helps protect the spheroid from immune attack. To improve spheroid viability and functional performance with emphasis on insulin secretion we implemented a glucagon-like peptide-1 (GLP-1) based genetic strategy in 𝛽TC-6 cells. Specifically, we engineered 𝛽TC-6 cells to express glucagon-like peptide-1 (GLP-1) via lentiviral transduction. This enables sustained, local (auto/paracrine) delivery of an incretin that potentiates glucose-stimulated insulin secretion (GSIS) while supporting 𝛽-cell survival. We co-cultured GLP-1 transduced 𝛽TC-6 cells and endothelial cells to make self-assembled spheroids using the hanging-drop method. We need to preserve endothelial–𝛽-cell crosstalk, which stabilizes the 𝛽-cell phenotype and primes constructs for vascular integration after implantation. The total active GLP-1 protein from transduced 𝛽-TC-6 cells was confirmed and showed increase in stimulation index. The overall design aim was that (i) engineering 𝛽-TC-6 cells with GLP-1 would improve insulin secretion, (ii) co-culture with endothelial cells would provide revascularization, and (iii) coating the spheroid with GelMA nanogels would support immunoisolation. As a result, functional enhancement and immunoprotection are brought together in one graft-ready spheroid.This thesis study contributes to the research field of type-1 diabetes treatment by engineering and improving insulin secreting co-cultured pseudoislets with immunoisolation functions.
Cardiovascular device-induced blood cell trauma investigated using a hemostable flow loop
In this doctoral dissertation, a series of experimental and biological models were developed to improve the hemomechanical compatibility of blood-contact biomedical devices and bring in vitro test conditions closer to clinical reality. The studies encompass both engineering solutions to reduce device-induced blood damage and innovative approaches to preserving the biological integrity of blood under experimental conditions. In the first phase, considering the inadequacy of conventional flow-loop systems commonly used in in vitro testing to reflect clinical conditions, a metabolically sustainable system integrating nutrition, oxygenation, and dialysis modules was designed. In this system, human blood was circulated for 12 and 48 hours, and biomarkers such as hemolysis (NIH, pfHb, bilirubin, haptoglobin), inflammation (IL-8, TNF-α, C3a), coagulation (fibrinogen, TAT), platelet and endothelial activation (β-TG, vWF), and ferritin were monitored. While pH decreases, lactate increases, and inflammatory/coagulatory parameters increased in the control circuit, these parameters remained stable or decreased in the dialyzed circuits, and hemolysis was found to be 77–81% lower. These results demonstrate that long-term testing systems that can preserve the biochemical integrity of blood can provide a more reliable platform for predicting the clinical performance of devices. In second study, a new centrifugal pump design was developed that reduces blood damage by approximately 30% compared to the FDA-recommended reference pump, and its performance was evaluated in flow-loop experiments with fresh human blood. Comparisons with commercial pumps showed that while hemolysis and biomarker levels exceeded tolerance limits in the FDA reference pump, the optimized design reduced hemolysis by 68% and performed similarly to commercial devices in terms of inflammation, coagulation, and platelet activation. These findings demonstrate that improvements in device design can provide clinically meaningful biological benefits. In third study, a new methodology based on an organ culture approach is presented, treating blood not as a passive fluid but as a metabolically active and living system. Viability was maintained with blood gas analyses and nutritional solutions in a flow system constructed using standardized cardiovascular bypass components, and oxygenator and pump prototypes were tested. Throughout the experiments, erythrocyte deformability, hemolysis indices, enzyme activities (glutathione peroxidase, superoxide dismutase, catalase), and 2,3-diphosphoglycerate levels were maintained, and minimal submicron particle release was observed. This approach reduced biological variation in blood injury experiments, resulting in more realistic results. In the last work, the necessary infrastructure for genetic modulations to increase mechanical stress resistance in erythrocytes differentiated from hematopoietic stem cells was investigated. The differentiation mechanism of cells was investigated using the CD235a surface marker, the fluorescently labeled siRNA uptake system was validated using electroporation, and the membrane elasticity of control erythrocytes differentiated from stem cells was measured by micropipette aspiration. Findings showed that cells in suspension had a higher differentiation rate, but this rate decreased as time and passage number increased. Furthermore, a system for shaping erythrocyte biomechanics through genetic manipulations was developed, and it is envisioned that this method could create a new research platform that could be used both in basic biology studies and in hemocompatibility testing of blood-contact devices. Overall, this thesis aims to improve hemomechanical stability through design optimizations of blood-contact devices, while also reducing blood damage through metabolically sustainable test systems and genetically modified cell models. The obtained results contribute to the development of new standards in the preclinical evaluation of cardiovascular devices, providing important scientific data aimed at improving both patient safety and the effectiveness of biomedical devices.
Novel signal processing approaches for cortico-cortical evoked potentials from stereo-electroencephalography to improve seizure onset zone localization in drug-resistant epilepsy
Drug-resistant epilepsy (DRE) remains a major clinical challenge, with many patients continuing to experience seizures despite advances in surgical interventions. Accurate delineation of the seizure onset zone (SOZ) is essential for optimizing surgical outcomes, yet current methods relying on electroencephalography, imaging, and invasive recordings are often limited by network-level complexity and inter-patient variability. Cortico-cortical evoked potentials (CCEPs) derived from stereo-electroencephalography (SEEG) provide valuable insights into brain connectivity and have been investigated as potential markers of epileptogenic tissue. Traditional analyses have focused on early and late negative deflections (N1/N2), but these components suffer from limited sensitivity, specificity, and generalizability across patients and cortical regions. In this study, we propose an advanced signal processing framework that moves beyond fixed windows and simple peak amplitudes. By extracting a broader set of features—including energy, line length, entropy, and Root Mean Square metrics—we aim to more reliably distinguish epileptogenic from non-epileptogenic regions. This approach emphasizes individualized, data-driven characterization of evoked responses to refine surgical planning. Ultimately, our framework seeks to reduce unnecessary resections, improve precision in SOZ localization, and enhance outcomes for patients with DRE.
Glioma-on-a-chip for investigating gliomagenesis and temozolomide treatment under static and continuous flow conditions
Gliomas constitute the most prevalent class of primary cancers in the central nervous system and arise from the brain's supportive glial lineage. Therapeutic outcomes remain suboptimal, mainly owing to the tumor's highly invasive phenotype and its heterogeneous microenvironment. Among them, glioblastoma (GBM) is associated with dismal prognosis and high mortality despite current multimodal clinical management. Advancing effective treatment strategies requires a deeper understanding of GBM pathobiology. Conventional two-dimensional (2D) static culture systems fail to capture the complexity of the tumor microenvironment. They cannot emulate the dynamic biochemical and biophysical cues present in vivo, underscoring the need for more physiologically relevant platforms. Furthermore, the inabilities of conventional systems motivate studies of the development of patient-tailored treatments, prompting the emergence of diverse three-dimensional (3D) microfluidic systems designed to model glioma biology. Microfluidic organ-on-chip technologies, which enable continuous perfusion, offer the capacity to replicate in vivo–like metabolic activity and microenvironmental conditions. Microfluidic platforms that recapitulate key features of the tumor microenvironment hold considerable promise for generating physiologically relevant in vitro glioma models, enabling systematic analyses of treatment responses. Such platforms may reduce the reliance on in vivo animal studies and facilitate the evaluation of drug regimens. In this thesis, a biologically realistic glioma model is developed by integrating GBM cells, an engineered hydrogel, and a custom-designed microfluidic chip. Additionally, the chip system developed in this study offers ease of use due to its simplified design, which allows for the injection of cell-laden biomaterial using syringe needles. Given that hyaluronic acid (HA) is a significant component of the GBM extracellular matrix and plays a key role in tumor progression, HA is selected in combination with gelatin methacrylate (GelMA) as the hydrogel system to recapitulate native GBM microenvironmental cues. GBM cells were subsequently cultured within the PDMS-based microfluidic platform and evaluated in terms of cell viability and gene expression profiles. Molecular biomarkers of gliomagenesis (e.g., EGFR) were investigated for human GBM cell lines (e.g., U87-MG) cultured under static and continuous flow conditions. Temozolomide treatment studies were conducted to evaluate drug responsiveness within the dynamic culture system. This thesis aimed to overcome the limitations of traditional 2D culture by establishing a 3D, dynamically perfused glioma-on-a-chip system, which integrates a hydrogel with a chip-based architecture that more faithfully replicates GBM tumor physiology to assess drug responses. It provides a robust framework for interrogating glioma biology and assessing therapeutic strategies.
Kanser tedavisi amaçlı nano parçacıkların sentezi ve değerlendirilmesi
Nanotechnology-based drug delivery systems have emerged as promising tools in cancer therapy, offering improved drug targeting, reduced systemic toxicity, and enhanced therapeutic efficiency. Among various nanomaterials, iron oxide nanoparticles (IONPs) are widely recognized for their biocompatibility, magnetic responsiveness, and surface modification potential. In this study, quercetin-loaded iron oxide nanoparticles (Q-IONPs) were synthesized and evaluated for their physicochemical properties and cytotoxicity against the MCF-7 breast cancer cell line. The nanoparticles were prepared using the co-precipitation method by mixing ferrous sulfate (FeSO₄) and ferric chloride (FeCl₃), followed by the addition of sodium hydroxide (NaOH) to form iron oxide nanoparticles. Quercetin was subsequently incorporated to enhance the formulation's therapeutic efficacy. Particle size analysis revealed an average hydrodynamic diameter of 394.2 ± 6.5 nm, confirming the formation of nanosized particles. Preliminary pH monitoring suggested good stability of the nanoparticles under near-physiological conditions. The cytotoxicity of Q-IONPs will be further assessed against MCF-7 cells using the MTT assay to evaluate their potential as anticancer agents. The outcome of this research is expected to provide valuable insights into the development of quercetin-based iron oxide nanoparticles as a promising nanocarrier system for targeted cancer therapy.
FGD-pet görüntüleme kullanarak alzheimer hastaliğinin radyomik analizi
Alzheimer's disease (AD) demands more advanced and personalized diagnostic methods. This dissertation proposes a radiomics-driven framework using FDG-PET to enhance the diagnosis, staging, and risk evaluation of AD. By integrating image-derived features and machine learning, we aim to facilitate early, non-invasive, and individualized assessment. We developed a fully automated brain radiomics platform capable of distinguishing between CN, MCI, and AD individuals. The hippocampus, entorhinal cortex, and amygdala emerged as key discriminative regions. Our simplified FDG-PET model achieved an AUC of 0.853 for predicting amyloid positivity, a critical pathological hallmark of AD, using features from the hippocampus, inferior parietal lobule, and isthmus cingulate. The platform was further extended for ApoE4 genotype prediction, achieving an AUC of 0.945 with features extracted from the hippocampus, amygdala, thalamus, and pars orbitalis. We also investigated hippocampus-amygdala connectivity, identifying robust biomarkers such as Shape Mesh Volume and GLDM Small Dependence Low Gray Level Emphasis (AUC = 0.88). Subregional analysis of hippocampal and amygdaloid structures revealed additional radiomic features, including GLRLM Long Run Emphasis and GLDM Small Dependence Emphasis, which differentiate AD from MCI and CN, indicating early microstructural and metabolic changes prior to visible atrophy. Our findings establish FDG-PET radiomics as a reliable, non-invasive imaging biomarker for diagnosing and monitoring AD. The proposed framework enables risk stratification and supports clinical decision-making, paving the way for preventive and personalized AD management.
Yumuşak kısım yapısı ve sert kısım miktarının poliüretanürelerin yüzey ve yığın özellikleri üzerindeki etkisi
Due to their interesting combination of bulk and surface properties segmented thermoplastic polyurethanes (TPU), polyureas and polyurethaneureas (TPUU) find wide range of applications in many diverse fields. One of the emerging applications of TPUUs include their usage as biomaterials in blood contacting applications. This is mainly due to the possibility of designing and synthesizing TPUUs with controlled bulk and surface properties that possess very good blood and tissue compatibility. [1] The main goals of this study were the investigation of the influence of; (i) soft segment (SS) structure, (ii) SS molecular weight and (iii) hard segment (HS) content on the morphology and bulk and surface properties of TPUUs. In addition, another aim was to investigate the relationship between the surface energies of copolymers and their resistance to biofilm formation. A large number of segmented thermoplastic poly(urethaneurea)s (TPUU), polyurethanes (TPU) and polyureas (PU) based on five different SS were synthesized by using the conventional two step "prepolymer" polymerization method (or in one step if the polymer was non-chain extended) and characterized. Bis(4-isocyanatocyclohexyl)methane (HMDI) was used as the diisocyanate and 2-methyl-1,5-diaminopentane (MDAP) or 1,4 butanediol (BD) was used as the chain extender. Five different SS which were used in this study included poly(ethylene oxide) glycol (PEO), poly(propylene oxide) glycol (PPO), poly(tetramethylene oxide) glycol (PTMO), aminopropyl and hydroxyhexyl terminated polydimethylsiloxane (PDMS) and a hydroxy terminated polyfluoroether (PFE) oligomer (Fluorolink E10-H®). HS contents of the copolymers were generally kept constant at 20 and 30% by weight with a few exception. To investigate the influence of the molecular weight, SS oligomers with two different molecular weights of 1,000 and 2,000 g/mol were used during the synthesis. The bulk and surface properties of all polymers were characterized by using a large number of techniques, which included; ATR-FTIR (Attenuated Total Reflection Fourier Transform Infrared), DSC (Differential Scanning Calorimetry), SAXS (Small Angle X-ray Scattering) and stress strain analysis, AFM (Atomic Force Microscopy), XPS (X-ray Photoelectron Spectroscopy) and static water contact angle measurements. Selected copolymers with different surface energies were also tested for biofilm formation. Results obtained indicated extensive biofilm formation on all samples regardless of their surface properties. Characterization results showed that polyether based copolymers, especially those with PEO SS, displayed poor microphase separation when compared with PDMS and PFE based copolymers. This is expected since the polyethers used in this study have higher solubility parameters and ether groups can form hydrogen bonding with urethane and urea groups, which is not possible in case of PDMS and PFE. Surface characterization by contact angle measurements showed dramatic differences depending on the SS structure and molecular weight. As indicated by XPS studies, in general the soft segments tend to migrate to the polymer surface and affect the hydrophobicity and hydrophilicity of the copolymer depending on their solubility parameters. The extent of biofilm formation was not affected by the surface energy differences within the copolymers. Many alternatives for the bacterium sticking mechanism on surfaces have been proposed in the literature. [2] Some studies suggest that bacterium tend to stick on hydrophilic surfaces[3], while other studies suggest that bacterium tend to stick on hydrophobic surfaces [2]. It should also be noted that the sticking mechanism of every strain of bacterium is different [4], which makes this concept even more challenging to explain. Therefore our study is a contribution to the literature on this topic and suggests that the sticking mechanism of Staphylococcus aureus 700698 strain of bacterium is not affected by the surface of the polymer being hydrophilic or hydrophobic.
CRISPR-Cas9 aracılığı ile kromatin modifiye eden genlerin insan hücre yeniden programlanmasında incelenmesi
Reprogramming of somatic cells to pluripotency via four transcription factors, Oct4, Sox2, Klf4, and c-Myc (OSKM) involves extensive remodeling of the epigenome which is carried out by a number of chromatin modifiers. A number of these genes have been studied in the context of reprogramming and defined as barriers or essential regulators of this process. However, established protocols limit a comprehensive examination due to the susceptibility of shRNA vectors to proviral silencing which accompanies reprogramming, and the unavailability of human knock-out cell lines. Therefore, we hypothesized that pooled CRISPR-Cas9 knock-out libraries can enable systematic investigation of chromatin modifiers and reveal their role in different steps of reprogramming by enabling permanent gene modifications. To this end, we constructed a CRISPR-Cas9 knock-out library targeting the 247 chromatin modifiers including chromatin remodelers, writers, readers and erasers of histone and DNA modifications. We utilized this library to generate heterogeneous cell populations harboring putative chromatin modifier knock-outs, which were then reprogrammed with the delivery of OSKM. FACS-based enrichment of TRA-1-60 positive cells, and low copy exogenous retroviral EGFP silencing was utilized to collect emerging iPSCs at different time points of reprogramming. The abundance of CRISPR guide RNAs in isolated cells were determined by next generation sequencing. Analysis of relative enrichment of specific guide RNAs confirmed the majority of the known reprogramming regulators and identified novel stage specific barriers and essential regulators for human somatic cell reprogramming. These include PAXIP1, BRD2 and USP22 as barriers, and CHAF1A, KDM8 and PRMT5 as essential regulators. In addition, functional analysis based on class of genes revealed that various MLL complexes act as barriers, and BAD, SWI/SNF, and MOZ/MORF complexes act as essential regulators for reprogramming. Based on the screen results, stage specific combinatorial use of small molecule inhibitors enabled accelerated and more synchronous efficient reprogramming. Taken together this study establishes roadblocks of reprogramming through chromatin landscape, and can guide more efficient reprogramming strategies to be formulated.
Medulloblastoma'da kromatin değiştirici enzimlerin fonksiyonlarının incelenmesi
Medulloblastoma is the most common pediatric brain cancer and it consists of four main molecular subgroups, which are Wingless (WNT), Sonic Hedgehog (SHH), Group 3 and Group 4. These subgroups have different transcriptional, cytogenetic and mutational spectra, making medulloblastoma a complex disease. Current therapy protocols for medulloblastoma include surgical resection, craniospinal irradiation and chemotherapy. Although current treatments result in high overall survival, many survivors experience severe neurological disorders. Therefore, targeted and more efficient therapies are necessary for the treatment of medulloblastoma. Genomic studies revealed that several chromatin modifying enzymes (CMEs) such as histone methyltransferases (HMTs), histone demethylases (HDMs), histone acetyltransferases (HATs) and histone deacetylases (HDACs) are mutated and/or differentially expressed in medulloblastoma. However, the roles of CMEs in the initiation and progression of medulloblastomas are ill-defined. To this end, we mainly focused on the epigenetics of medulloblastoma to develop novel and more effective therapeutic options. Firstly, we investigate the roles of chromatin modifiers in medulloblastoma by utilizing a chemical library targeting different chromatin modifying enzymes. Our screen revealed some potential inhibitors, namely GSK-J4, IOX-1, Belinostat, Vorinostat, 5-Azacytidine, ML324, SGC0946, Trichostatin A and Chaetocin, that induced cell death in medulloblastoma cells significantly. To investigate whether these drugs are specific to cancer cells, we tested selected drugs in a dose-dependent manner in non-malignant BJ Fibroblasts and revealed that they were relatively non-toxic to normal cells. Since the roles of histone demethylases are barely defined in medulloblastoma, we focused on KDM6A and KDM6B, which are targets of GSK-J4 and IOX-1. To this end, we targeted KDM6A and KDM6B by shRNAs and examined whether their loss changed the growth rate medulloblastoma cells. However, we did not observe any changes in the proliferation rate of MB cells upon KDM6A and/or KDM6B loss. Although many medulloblastoma tumors respond to chemotherapy well, there are still many medulloblastoma patients who do not respond to standard of care chemotherapy. As it has been identified that many chromatin modifiers are mutated and/or differentially expressed in the most aggressive and metastatic subgroups (Group 3 and Group 4), we speculated whether chromatin modifiers play role in resistance of medulloblastoma cells to chemotherapeutic agents. From those, vincristine is the main chemotherapeutic agent used in different treatment protocols, we decided to establish a vincristine-resistant medulloblastoma cell line by dose-escalation method to elucidate the function of CMEs in therapy resistance. We performed another drug screen in parental and newly established vincristine-resistant cells and identified that 8 different HDAC inhibitors (Trichostatin A, Rocilinostat, CXD101, Tubastatin A HCl, Belinostat, Romidepsin, PCI-24781 and Mocetinostat), 2 histone demethylase inhibitors (IOX-1 and KDOBA67), 2 kinase inhibitors (5-Iodotubercidin, SGI-1776), MAZ1805 (Halofuginol) and MAZ1392 induced cell death both in parental and vincristine-resistant cells significantly. Besides, we performed combination treatment with epigenetic drugs and vincristine and discovered that A-395, CBP/BRD4, GSK-J5, GSK343, GSK864, LLY-507, OF-1, SGC-CBP30, SRT1720 and UNC2400 induced cell death of resistant populations when they were combined with vincristine.
Nakil edilen adacıkların vücuttan reddedilmesini önlemek amacıyla bağışıklık sisteminden ayrı tutulabilen bir bölgesel mikroortam dizayn edilmesi
The development of tolerance induction approaches via immune engineering that can restore and/or replace non-functional tissues and organs represents the leading front of emerging regenerative therapies. Type-1 diabetes (T1D) is an organ-specific autoimmune disease characterized by destruction of pancreatic β cells, which are insulin-secreting cells by autoreactive T cells and other immune cells. Loss of β-cell, thus insulin, makes patients dependent on exogenous insulin or to overcome this need; transplantation of pancreas or intact islets. One of the promising approaches used for treatment of diabetes is the transplantation of islets; however, it also comes with its pitfalls. First and most obvious one is the limitation of donor source. In addition, transplantation of islets or entire pancreas requires suppression of the immune system to prevent graft rejection. This suppression is achieved through immune suppressor drugs, which leaves the body defenseless against infections and increases its susceptibility to other complications such as cancer. Considering all these limitations, immunotherapeutic strategies have focused on restoring immunologic self-tolerance, thus removing the problem at it roots; preventing β cell destruction by patients's own immune system. The main focus of this approach is regulatory T cells (Tregs), which are essential cells in suppression of autoreactive immune responses and maintenance of self-tolerance. Stellate cells (SCs) have various effects on the immune system such as recruitment of Tregs and induction of T cell apoptosis. Besides, they can promote vascularization, secreting vascular endothelium growth factor (VEGF). Some chemokines are also key modulators in recruitment of Tregs. Macrophage-derived chemokine or C-C motif chemokine ligand 22 (MDC/CCL22) is one of the novel chemokines used for Treg recruitment by binding to CCR4 receptor on their membrane. In this study, we designed an immune privileged microenvironment around implantable insulin secreting islets site to provide local graft tolerance and to overcome limitations associated with donor cells. We focused on achieving local immunosuppression through overexpression of CCL22 proteins by SCs, which recruited immunosuppressive Tregs. We prepared insulin-secreting pseudoislets through aggregation of mouse insulinoma 6 (MIN6) cells as a model system to mimic naïve islet morphology. Our results demonstrated that transfected SCs can secrete CCL22 and recruit a population of Tregs towards the implant in vivo. This study is promising to provide fundamental understanding of the SC-islet interaction, ligand synthesis and transport from stellate cells at the graft site for ensuring local immune tolerance to target Type I diabetes. Our results also establish a new paradigm for creating tolerable grafts for other chronic diseases such as diabetes, anemia, cancer, CNS diseases and advance the science of graft tolerance.
K-Ras proteini ve onkojenik mutasyonları üzerine kapsamlı bir çalışma: Dinamik bir bakış açısı
K-Ras is the most frequently mutated protein in human cancers driving cancer initiation, progression and drug resistance, directly leading to nearly a million deaths per year. Sadly, there are still no drugs in that directly target mutant K-Ras in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting it. However, despite extensive characterization, the regulatory mechanisms of K-Ras dynamics remain elusive. Since protein function is related to its dynamics, understanding these mechanisms can present novel opportunities for identifying target sites on mutant K-Ras surface. In this work, we investigate the regulation mechanisms of K-Ras dynamics and the effects of nucleotide binding and mutations on these mechanisms using extensive molecular dynamics (MD) simulations. We applied different MD simulation data analysis techniques to compare the dynamic characteristics of both active and inactive forms of wild-type K-RasWT and mutant K-RasG12D, the most recurrent mutant in cancer patients. Our results on K-RasWT showed excellent agreement with experimental data and served as a reference point for K-RasG12D analysis. Then, we demonstrated how G12D mutation induces structural and conformational changes that result in characteristic correlated motions in active K-RasG12D. Moreover, we developed a novel conditional time-delayed correlations (CTC) based approach to predict causal relationships in regulation of K-Ras dynamics. CTC analysis identified the regulatory sites that control K-Ras dynamics. Finally, we identified a novel drug target pocket in active K-RasG12D and screened a small molecule library against it using docking techniques. Our study draws a complete picture of the regulation of K-Ras dynamics. We anticipate that the identified regulatory sites on active K-RasG12D can present novel opportunities for direct targeting of K-RasG12D in future drug discovery efforts.
PRISM'in geçmiş CAPRI turları ile değerlendirilmesi
Proteins are key elements of a cell to perform the wide range of molecular and cellular activity. Proteins perform their function through binding to other proteins, DNA, RNA, and small molecules. Therefore, predicting how a protein interacts with its binding partners is one of the most important objectives of structural biology. As a result of the improvements in experimental structure determination methods, the number of individual protein structures in PDB has increased vastly. However, the number of complex structures does not increase as fast as the individual proteins which creates demand for new approaches to predict complexes from the individual protein structures. Currently, there are a lot of computational approaches to predict the complex structures. Critical Assessment of Prediction of Interactions (CAPRI) is a well-known community-wide experiment with the purpose of establishing a routine which allows testing the performance of several different docking algorithms created. The success rate of predicted structures is verified by the several evaluation criteria determined by the CAPRI association. Those criteria are interface and ligand rmsds (I-rmsd, L-rmsd), native residue contacts and number of clashes. In this study, I assessed the performance of PRISM (Protein Interaction by Structural Matching) using CAPRI evaluation criteria. The main objectives were to determine how much PRISM is successful in predicting the complex structures of available CAPRI targets and to force the limits of PRISM by stretching the parameters of PRISM. PRISM could not predict the correct complex structures for 33% of targets majority of which correspond to homodimers and enzyme/inhibitor complexes. The results also indicate that considering just the structures with the negative energy score results in the loss of 36% of successful predictions implying a problem in the scoring function. For further testing, RosettaDock was used as an alternative scoring function. Both scoring approaches yielded a correlation. To increase the success rate, some parameters of PRISM were changed however, no significant improvement has been achieved.