Izmir Institute of Technology

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Adsorption of methane reformer off-gas components in a column packed with Cu, Al,Ti and Zn based organic frameworks
(Izmir Institute of Technology, 2016-12) Kanaltı, Gaye; Çakıcıoğlu Özkan, Seher Fehime
Within the past decade, CO2 emissions from fossil fueled power plants has accelerated rapidly as a result of the increase in energy consumption associated with industrial development all over the world. Beyond the necessity of reduction in CO2 emissions, concerning on the crude oil reserves depletion induced the urgent need of transition to more efficient, renewable, cleaner and cheaper fuel, hydrogen. In the world, most of the hydrogen is produced by hydrogen-rich stream methane reformer (SMR) off gas streams composed of 80-60% H2, 15-25% CO2, 3-6% CH4 and 1-3% CO, thereby separation of SMR components became more of an issue. In this study, adsorption based separation of SMR components were investigated in a column packed with copper (CuTPA, (SLang: 776 m2g-1)), aluminum (AlTPA, (SLang: 1330 m2g-1)), titanium (TiTPA, (SLang: 1835 m2g-1)) and zinc (ZnTPA, (SLang: 1023 m2g-1)) based organic frameworks (MOFs). The pure gas adsorption studies on equimolar CO2/H2, CH4/H2 and CO/H2 systems and the equimolar mixture of CO2/CH4 system were carried out and the experimental breakthrough curves were obtained at three different feed flow rates (10, 20 and 30 mL/min) at three column pressure (1, 5 and 10 bar) at 303 K. The highest adsorption capacities of all MOFs were achieved at 30 mL/min of feed rate and 10 bar operating pressure, at these conditions the non-adsorptive behavior of hydrogen on the aforementioned MOFs was ensured. The amounts of CO2 adsorbed were calculated as 1.61, 5.54, 5.20 and 2.11 mmolCO2/g, while adsorbed CH4 amounts were 1.50, 3.16, 3.25 and 1.90 mmol CH4/g and the adsorbed CO amounts were 1.47, 2.59, 1.91 and 1.83 mmol CO/g on CuTPA, AlTPA, TiTPA and ZnTPA, respectively. The highest selectivity for CO2 over CH4 was attained on TiTPA as 8.0 at 10 mL/min feed rate of CO2/CH4 mixture at atmospheric column pressure and 303 K. The experimental adsorption isotherms of SMR components were fitted well with Langmuir and virial models and the best fitted model parameters were evaluated for each MOF.
An analytical study of creativity in architectural design:case study of national architectural awards
(Izmir Institute of Technology, 1999) Kandilci, Ebru; Eyüce, Ahmet
The subject of the thesis is in general based on the concept of creativity and specialised on creativity in the architectural design process. The topic, which is taken into consideration as the investigation of architectural creativity, begins with the definitions of creativity concept related with the design approaches. Throughout the evolution of these definitions, the common denominator of psycology, sociology, behavioral sciences and architectural design concepts are tried to be clarified. The creativity studied on the basis of concept, individuals and theories later developed as deciphering the classification of effecting channels of architectural design process.The classification consists of three main parts: 'personal channels' involving childhood, fantasy, imagination, metaphor, intelligence, self confidence, 'social channels' including education, national culture-history, religious factors, client, and 'environmental channels' that involve nature, material and climate. The concrete examples of this study are chosen among the projects of the leading architects in Turkiye. The first parameter for elimination is National Architectural Exhibition and Awards. Projects among National Architectural Exhibition and Awards are selected according to the criteria for architectural creativity related with the concepts such as originality, newness and contemporaneity which are not very far apart from the criteria of the jury. Concept of originality also includes sub-titles such as architectural language, conceptual approach, technology, material and at each sample different concepts primarily appears. To consider the existence of these criteria provides the evaluation of the samples related with the fact of creativity.
Antimicrobial and antioxidant activities of olive leafextract and its food applications
(Izmir Institute of Technology, 2010) Aytul, Kerem Kaan; Korel, Figen
In this study, aqueous/ethanol extract of olive leaves (OLE) was examined for its antimicrobial and antioxidant activities and its possible food applications. In the first part of the study, relative antioxidant capacity and total phenol content of the extract were determined and found as 966 .g ascorbic acid eq./mg and 197.42 mg GAEq/g sample, respectively. In the second part, microdilution assays were conducted by 96 well plate for OLE to find minimum inhibition concentration (MIC) against Gram (+) and Gram (-) bacteria. The most susceptible bacteria were Escherichia coli, Listeria innocua and Staphylococcus carnosus. In the third part OLE was applied to raw beef cubes with 1%, 2% and 3% (v/w) concentrations to examine its antimicrobial and antioxidant effects. The results clearly indicated that usage of 2% and 3% OLE had the beneficial effect in controlling the microbial load, total viable and coliform counts, of beef cubes during 9 days of storage at 4 C. The 2% OLE treatment applied to beef cubes also delayed the oxidative deterioration compared to the other samples. As the last part of the study, 300 ppm OLE was applied to sardine (Sardina pilchardus) fillets as a marinade component. Results indicated that OLE was effective in controlling microbial load of sardine fillets and also delayed the oxidative deterioration and total volatile base nitrogen formation in the fillets during marination process.
Antimicrobial, antioxidant, antiproliferative and cytotoxic activities of aronia fruit extract
(01. Izmir Institute of Technology, 2023-07) Tanağardı, Dilaranur; Baysal, Ayşe Handan; Sezgin, Efe
Aronia melanocarpa contains high amounts of phenolic compounds, especially anthocyanins. Because of its high chemical content and significant antioxidant action, this food is known as a functional food, and its use is spreading worldwide. Within the scope of this thesis research, studies were carried out on Aronia melanocarpa dry extract and liquid extract. For these purposes, chromatographic and chemical profile were determined in detail by HPLC (High-Pressure Liquid Chromatography), Fourier-Transform Infrared Spectroscopy (FTIR) and Q-TOFF- MS (Quadrupole Time of Flight Mass Spectrometry), and significant bioactive were determined. Spectroscopic methods were used to characterize phenolic, anthocyanin, and flavonoid components. Aronia melanocarpa dry and liquid extracts were tested for antioxidant activity using DPPH and ABTS methods. The antioxidant potential of the Aronia melanocarpa dry and liquid extracts studied is high. To test the antiproliferative and cytotoxic effects, cytotoxic studies were performed on the CaCo2 cell line. Cell migration was also studied in HUVEC and HaCat cell lines. The antimicrobial activity of Aronia melanocarpa dry extract and liquid extract was tested against Saccharomyces cerevisiae, a yeast species, and bacterial strains of Staphylococcus aureus, Escherichia coli O157:H7, Salmonella Typhimurium. The extracts analyzed showed an antimicrobial effect on the tested bacteria at different concentrations. The results obtained in this study emphasize that the tested Aronia melanocarpa dry extract and liquid extract have antimicrobial properties. Chromatographic, chemical, and cytological data reveal that Aronia melanocarpa liquid and dry extracts can be used as antioxidative and antiproliferative products as food supplements in the health field.
Applications of Petri nets
(Izmir Institute of Technology, 2008) Yılmaz, Buket; Ufuktepe, Ünal
Petri nets are powerful formalism for modeling a wide range of dynamic systems and system behaviors. This thesis surveys the basic concept and application of Petri nets. The structure of Petri nets, their marking and execution and several examples of Petri net modeling. In this thesis we research into the analysis of Petri nets. Also we give the structure of Reachability graphs of Petri nets and their advantages for analyzing the Petri nets. The reachability problem for Petri nets is the problem of finding if Mn 2 R(M0) for a given marking Mn in a net (N,M0).We present several different kinds of Petri nets, together with computer tools based on Mathematica. We give the Mathematica commands for Reachability problem and also we created Mathematica commands for Incidence matrix of Petri nets. We study the concept of Petri nets and applications of Petri nets.We especially focus on Biological applications on Petri nets and we work on modeling of Hashimoto.s Thyroiditis in Petri Nets.
Authentication and prediction of some quality parameters of alcoholic beverage rakı with infrared spectroscopy
(Izmir Institute of Technology, 2011) Yücesoy, Dila; Özen, Banu
Mid-infrared spectra of thirty- two Rakı samples of different brands, two types of Ouzo were collected and several chemical parameters were measured with analytical and instrumental methods. Moreover, Rakı samples were adulterated with methanol at 0.5-10% (vol/vol) and IR spectra were also obtained. Aims of this study are to classify Rakı samples according to raw material of Rakı and processing type, to predict some quality parameters of Rakı from IR spectra and also to detect adulteration of methanol in pure Rakı by using Fourier transform infrared spectroscopy in association with multivariate chemometric techniques and SIMCA. All samples were used to classify with respect to grape types (fresh or dried), raw material (only suma or suma and ethanol) and production process (double or triple distilled) by chemometric models. No clear classification could be found as parameters investigated because of predominant of alcoholic content in Rakı. In quantification analysis; pH, brix, electrical conductivity, total phenol and sugar content were determined with analytical reference methods for pure samples, then PLS were used to construct models to establish relationships between reference methods and FTIR spectra and to predict these quality parameters from spectral data. After PLS regression, highly good models were developed for brix and sugar. For adulteration analysis, six different Rakı samples were adulterated. First, PCA was used to detect Rakı samples adulterated with methanol. Then, PLS multivariate calibration model was constructed to determine the adulterant methanol content in Rakı . Consequently, successful results were obtained for detection of methanol in Raıı samples.
Automatic identification of evolutionary and sequence relationships in large scale protein data using computational and graph-theoretical analyses
(Izmir Institute of Technology, 2012) Doğan, Tunca; Karaçalı, Bilge
In this study, computational methods are developed for the automatic identification of functional/evolutionary relationships between biomolecular sequences in large and diverse datasets. Different approaches were considered during the development and optimization of the methods. The first approach focused on the expression of gene and protein sequences in high dimensional vector spaces via non-linear embedding. This allowed statistical learning algorithms to be applied on the resulting embeddings in order to cluster and/or classify the sequences. The second approach revised the pairwise similarities between sequences following multiple sequence alignment in order to eliminate the unreliable connections due to remote homology and/or poor alignment. This is achieved by thresholding the pairwise connectivity map over 2 parameters: the inferred evolutionary distances and the number of gapless positions in each pairwise alignment. The resulting connectivity map was disjoint and consisted of clusters of similar proteins. The third and the final approach sought to associate the amino acid sequences with each other over highly conserved/shared sequence segments, as shared sequence segments imply conserved functional or structural attributes. An automated method was developed to identify these segments in large and diverse collections of amino acid sequences, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. The method produces a table of associations between the input sequences and the identified conserved regions that can reveal both new members to the known protein families and entirely new lines. The methods were applied to a dataset composed of 17793 human proteins sequences in order to obtain a global functional relation map. On this map, functional and evolutionary properties of human proteins could be found based on their relationships to the ones bearing functional annotations. The results revealed that conserved regions corresponded strongly to annotated structural domains. This suggests the method can also be useful in identifying novel domains on protein sequences.
Automatic, fast and accurate sequence decontamination
(Izmir Institute of Technology, 2016-07) Bağcı, Caner; Allmer, Jens; Tekir, Selma
The introduction of massively parallel sequencing technologies was a revolutionary step in genomics. Their decreasing cost and powerful features have put them more and more on demand in the last decade. It is now possible to sequence even complete genomes of organisms, using massively parallel sequencing technologies even for small laboratories around the world. However, the power of this powerful technology comes with its challenges. The challenges are both in technological and computational side of the work. In this work, one of these computational challenges is addressed and a novel algorithm is offered to solve the problem. Sequencing by synthesis is one of the methods used in many different massively parallel sequencing instruments. This method utilizes the biological process of DNA replication and with the help of different means of detection, it allows sequencing a DNA molecule while it is replicated. Since DNA polymerase requires a primer to start the replication reaction, short oligonucleotide adapters are used in sequencing by synthesis methods to initiate the reaction. However, certain circumstances allow these adapters to contaminate final sequence reads. Several tools have been offered to trim adapters from reads; but all depend on the prior knowledge of the adapter sequence by the bioinformatician. In this work, an algorithm is offered to detect and trim adapters only using the sequences of reads, without relying on prior knowledge of adapter sequences. The algorithm was shown to perform better or on the same grounds with existing methods in terms of speed and efficiency.
Axiality in the process of space organization in architecture
(Izmir Institute of Technology, 1999) Dinçer, Özgür; Eyüce, Ahmet
The scope of this study, tries to explain the definition of the architectural axis and its influences in the process of space organisation with all due aspects to the strong relationships between geometry and architecture. In doing this, the roles of the architectural axis in the spatial evolution of the architectural history are also explained in accordance with its various characteristics in different eras.The study tries to reveal the direct and primarily effects of the architectural axis in development of the architectural form in parallel with the spatial evolution througout all the history of architecture. Some invariable concepts are explained by means of the geometrical characteristics of the axis to make these effects more obvious to understand.All these explanations are aimed to be enriched with the historical examples to justify the conceptual statements.As a result, the whole study tries to reach the idea that the axiality which is born with different use of the architectural axis in the process of space organisation has different meaning and it is interpreted differently in parallel with the social economic and cultural characteristics of the era that it belongs. This idea is shown as a main reason of the changes in building forms and their spatial characteristics in all architectural history.KEY WORDS: Geometry, Point, Line, Axis, Plane, Volume and Form, Space, Meaning, Verticality and horizontality, Power, Symbol, Symmetry, Asymmetry, Balance, Perspective, Aperspective.
Biocatalytic performance of carbonic anhydrase immobilized within polyurethane foam in water-miscible organic solvents
(Izmir Institute of Technology, 2013) Ayaz, İlyas Umur; Özdemir, Ekrem
The effects of water-miscible organic solvents such as acetonitrile and ethanol on the activity of free and immobilized bovine carbonic anhydrase (CA) were investigated. The CA was covalently immobilized within polyurethane (PU) foam by cross-linking. Although PU foam holds water almost 12 times of its weight, it was found that adsorption isotherm of moisture on PU foam was a Type III indicating that water and PU foam were non-interacting to each other. The activities for the free and immobilized CA were estimated using para-nitrophenyl acetate (p-NPA) as the substrate. The enzyme activities were estimated in increasing volume percents of organic solvent in Tris buffer (10-90%). p-NP, which is one of the products of the hydrolysis reaction of p-NPA, was characterized in the presence of organic solvents and it was observed that its aborptivities were decreased significantly as the organic solvent percentages were increased indicating that p-NP and the water-miscible organic solvent form a complex through mostly a hydrogen bonding. The free CA showed decreasing activity up to critical percentages of organic solvent (40-60%), and then exhibited an increasing activity. The immobilized CA showed decreasing activity in acetonitrile at percentages up to 50%, and then lost its total activity at higher acetonitrile percentages, however, the immobilized CA exhibited no activity in ethanol at percentages above 10%. Stability tests showed that the immobilized CA was dramatically inactivated in the organic solvents at percentages above 30% in shorter times. It was concluded that the water-miscible organic solvents severely perturbed the active site of the enzyme, thus denaturating the enzyme.
Biochemical and mechanical cues for osteogenic induction of stem cells on paper based scaffolds
(Izmir Institute of Technology, 2019-12) Karadaş, Özge; Özçivici, Engin; Özhan Baykan, Hatice Güneş
Tissue engineering aims to produce functional constructs with living cells that can fully integrate with the tissue when inserted into the body. Design of the scaffold and the choice of cell type that will be used for production of the tissue engineering construct are very important for the success of the application. For bone tissue engineering, incorporation of substances with antimicrobial properties can supply additional benefits. This dissertation seeks answers for two discrete questions in different chapters: Do carnosol and carnosic acid, phenolic antimicrobial compounds extracted from plants have cytotoxic effect on bone tissue derived cells and do the culture conditions (monolayer or 3D) effect the response of cells (Chapter 2); and how do application of a single type of mechanical force (vibration) and a combination of two forces (vibration plus fluid shear) affect the osteogenesis of tissue engineering constructs (Chapters 3 and 4)? The results of this research demonstrated that carnosol and carnosic acid had bacteriostatic effect at 60 µg/mL but this concentration value was highly cytotoxic for bone tissue derived cells. Nevertheless, when the same cells were incubated under 3D culture conditions their cytotoxic tolerance was higher. The supportive role of mechanical forces on osteogenic differentiation of stem cells on 3D scaffolds prepared by using filter paper, on the other hand, was demonstrated with the increase in osteoblastic gene expression, immunocytochemical staining and detection of mineralization by Alizarin red S staining and quantification. In conclusion this research showed the importance of biochemical and biomechanical cues on osteogenesis.
Bioethanol production from fungal sources using low-cost agro-industrial waste products
(Izmir Institute of Technology, 2012) Evcan, Ezgi; Tarı, Canan; Özen, Fatma Banu
In recent years, the rapid increase in environmental problems, greenhouse gas emissions, fuel prices and the unlimited consumption of fuel stocks made people search for some alternative energy sources. Bioethanol is one of the most popular alternative sources with its many beneficial features. Considering the sugar content of fruit pomaces, which are the waste of fruit juice industry, are very convenient and cheap fermentation raw materials for production of bioethanol. The aim of this study was to create a renewable alternative for fossil fuel and to provide a viable solution to multiple environmental problems simultaneously creating a sink for waste utilization and optimize bioethanol production from apple pomace hydrolysate using Trichoderma harzianum, Aspergillus sojae and Saccharomyces cerevisiae by statistical methods. Here, screening and optimization steps were conducted in order to determine the significant factors and their optimum levels. Factors such as inoculation rate of A.sojae and T.harzianum and agitation speed were considered as factor variables, whereas the response variable was bioethanol production. According to the results of the screening process, inoculation rate of S.cerevisiae was fixed as 4% and aeration method as vented. In the optimization step, levels of the other factors were enlarged. The highest bioethanol production and yield on substrate were 8.748 g/l and 0.946, respectively. Higher concentrations of inoculation rates of T.harzianum and A.sojae (6%) and agitation speed of 200 rpm led to maximum bioethanol production. Furthermore, the results pointed out that using cocultures because of its synergistic interactions is an effective way for production of bioethanol.
Bioinformatic analysis and biostatistical modelling of genetic interactions between microbiota and host
(01. Izmir Institute of Technology, 2020-12) Musa, Farid; Sezgin, Efe; 01. Izmir Institute of Technology
Advances in genome sequencing technology have revolutionized the study of microorganisms. Recent genome-wide association studies (GWAS) on gut microbiota revealed fascinating discoveries about the effect of microbiota on our health. In this thesis, Drosophila Melanogaster samples were used to investigate the associations between the host's genotype and microbiota. The meta-analysis of microbiota data was performed using PhyloMAF, a novel, and comprehensive microbiome meta-analysis framework. The resulting microbial abundance tables were analyzed using alpha and phylogenetic beta bio-diversity metrics, which were used in the microbiome GWAS study. Significant variant associations were further analyzed in the post-GWAS analysis. The results of our study show that several genomic variants are significantly associated with bio-diversity estimates. Among identified variants, few were found to be associated with more specific phenotypes. Particularly, the gene involved in folate transport and linked to folate malabsorption was found to be associated with Proteobacteria. The latter for its part was found to be one of the primary phyla containing the highest number of genes responsible for de-novo folate synthesis. Similarly, the fly gene related to immune function with the human homologous gene linked to the inflammatory gut disease was found to be associated with the Acetobacter genus. This genus based on the literature survey was found to be associated with an immune deficiency in a fruit fly. In summary, this research revealed captivating findings of genetic factors associated with fruit fly microbiota. The limitations and future directions were stated in order to provide the basis for future prospective studies.
Bioinformatics based approach to design a thermophilic P450 fot industrial biocatalysis
(Izmir Institute of Technology, 2019-12) Kestevur Doğru, Ekin; Sürmeli Eraltuğ, Nur Başak
Enzyme catalyzed biosynthesis of steroidal drugs is an important process for pharmaceutical manufacturing. Cytochrome P450 (P450) monooxygenases are important for hydroxylation of steroid structures because they can catalyze the oxidation of inactive carbon bonds with high selectivity and efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be used as biocatalyst for industrial production since it shows activity at high temperature and low pH conditions. In this work we aim to use CYP119 for selective hydroxylation of progesterone, which is not the original substrate of CYP119, for production of precursor molecules of important hormones like cortisone and aldosterone. Crystal structure of CYP119 (PDB ID: 1F4T) was used for selecting residues that were mutated according to structural alignment with other CYPs that can catalyze progesterone hydroxylation naturally. Progesterone-docking performed with CYP119 to identify residues that create clashes with substrate. Finally selected 12 residues (Leu69, Val151, Phe153, Leu155, Leu205, Ile208, Ala209, Thr213, Thr214, Val254, Thr257, Leu354) were mutated with PyRosetta program to Gly, Glu, Phe, Met, Ala, His, Arg and Ile. Progesterone-docking performed with using DockMCM Protocol of PyRosetta. We used two different starting coordinates of progesterone for docking and results were eliminated according to their energy scores. Best mutants were used for creating double/triple mutants and second round of docking and elimination process were performed with using double/triple mutant enzymes. Final number of 11 mutants with best scores were selected and their possible products were identified.
Boundary controller and observer design for Korteweg-de Vries type equations
(Izmir Institute of Technology, 2017-12) Arabacı, Eda; Özsarı, Türker
This thesis studies the back-stepping boundary controllability of Korteweg-de Vries (KdV) type equations posed on a bounded interval. The results on the back-stepping controllability of the KdV equation obtained in Cerpa and Coron (2013) and Cerpa (2012) are reviewed and extended to the KdV-Burgers (KdVB) equation. The stability of the KdVB equation is boosted to any desired exponential rate for sufficiently small initial data with a boundary feedback controller acting on the Dirichlet boundary condition. Moreover, the case that there is no full access to the system is considered. For these kinds of systems, an observer is constructed assuming an appropriate boundary measurement is available. The ideas about designing output feedback control for the KdV equation presented in Marx and Cerpa (2016), and Hasan (2016) are reviewed and extended to the KdVB model.
Cell separation in microfluidic devices
(01. Izmir Institute of Technology, 2022-07) Öksüz, Cemre; Tekin, Hüseyin Cumhur
Cell separation is used to separate homogeneous and individual cell classes from a heterogeneous cell population. The efficiency and purity of these separated cells are of great importance in personalized medicine, regenerative medicine, disease monitoring and drug testing as well as in the therapeutic and diagnostic research. In this thesis, different microfluidic approaches were presented for cell separation. With this regard, a closed channel vacuum-integrated microfluidic chip was developed using an air permeability of a Polydimethylsiloxane and density-based separation of microparticles was performed. Besides, a centrifugal microfluidic system, Spinochip, was developed with one reservoir as inlet and outlet for the first time and different fluid manipulations were shown in the system. The system was applied to clinical tests of hematocrit measurements and white blood cell estimation using real patient samples. The developed system offered correlated results with clinical results. In addition to closed channel microfluidics, negative-magnetophoresis microfluidic chip was demonstrated for the size-based separation of microparticles and cells. In this regard, capturing rate of breast cancer cells (MCF-7) and human monocyte cells (U937) was investigated. The results showed that the approaches presented here could promote to the microfluidic studies for size-based cell separation.
Ceramic microfiltration membrane design towards oil removal in metal industry wastewater streams
(01. Izmir Institute of Technology, 2020-12) Eren, Muhammet Şakir Abdullah; Çiftçioğlu, Muhsin; 01. Izmir Institute of Technology
Increasing water scarcity is an important threat to the whole world. The use of too much water during the production processes and the insufficient level of reuse of this water and the increasing quantities of oil containing waste generated in many industrial activities cause dangerous consequences for the environment. Highly concentrated oil-inwater emulsions are very harmful for aquatic life, soil, atmosphere and human health. Traditional treatment methods are not effective in the removal of emulsified oil droplets which have less than 20 µm of droplet size. Ceramic micro/ultrafiltration membranes have been explored and developed in recent years due to their superior advantages in oil containing water treatment/purification. The aim of this MSc study was to produce tubular ceramic supports and microfiltration membranes for the removal of oil from stable oil in water emulsions used as metal cutting fluids. The prepared metal cutting fluids were fed to the crossflow filtration system and the effects of experimental parameters such as transmembrane pressure (TMP), crossflow velocity (CFV) and oil content on membrane performance/permeate flux were investigated. The single/double layered coatings on the support surfaces were formed in the preparation of the microfiltration membranes by using stable 0.4 µm α-alumina suspensions. The 1 layer and 2 layers containing microfiltration membranes were heavily fouled and very low permeate fluxes were obtained in an hour of treatment. This was attributed to the formation of a thin oil layer on the microfiltration membrane surfaces. The reduction of the total suspended solids (TSS) and turbidity were determined as ~100 %. A stable permeate flux with a lower extent of membrane fouling and concentration polarization was obtained with 1% oil content and the support membrane and TMP=2 bars.
Characterization and modification of antioxidant proteins from plat materials
(Izmir Institute of Technology, 2005) Arcan, İskender; Yemenicioğlu, Ahmet
In this study, the radical scavenging and iron chelating capacity of proteins from heat treated (20 min at 90 oC) or thermally processed (20 min at 121 oC) chick-peas andkidney-beans were compared. Lyophilized crude protein extracts from chick-peas contained more protein (1.5-3 fold) and showed higher free radical scavenging (up to 2.3 fold) and iron binding capacity (up to 3 fold) than lyophilized crude protein extracts form kidney-beans. The thermal processing of chick-peas did not cause a significant change in the radical scavenging capacity of their lyophilized crude protein extracts, but improved the iron chelating capacity of these proteins almost 80 %. However, the thermal processing reduced both the radical scavenging and iron binding capacity of crude lyophilized proteins form kidney beans by 20-40 % and 60 %, respectively.Partial purification by ammonium sulfate precipitation or DEAE-cellulose chromatography increased the antioxidant capacity of thermally processed chick-pea proteins. The DEAE cellulose chromatography also showed the presence of 5 and 3 antioxidant protein fractions in heat treated and thermally processed chick-peas, respectively. Hot acidic hydrolysis at 80 oC for 30 min in presence of 1.5 M HCl increases the specific antioxidant activity of protein extracts, but causes the formation of undesired Maillard reaction products. Hot extraction at 85 oC for 30 min at pH 2.5 extracts the antioxidant proteins selectively, whereas 85 oC for 30 min at pH 9.5 extracts both antioxidant proteins and other proteins.
Characterization and utilization of injectable hydrogels for tissue engineering applications
(Izmir Institute of Technology, 2020-07) Güzelgülgen, Meltem; Arslan Yıldız, Ahu
Tissue engineering combines the knowledge of the engineering aspects with life sciences to improve human health. Recent studies in tissue engineering have focused on investigating biocompatible scaffold materials and design. Quince seed hydrogel(QSH) has been used in traditional and modern medicine for skin wound and burn treatments, synovial lubrication, cough and asthma removal, and oral drug delivery with its antioxidant potential and biocompatible aspects. This thesis focuses on developing QSH and evaluating its potential as an injectable hydrogel in treating bone tissue defects as a totally new tissue scaffold and also as a promising tissue filling material. For this purpose, QSH scaffold optimization was carried out using various concentrations of hydrogel and crosslinkers which were glutaraldehyde(GTA) and 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide(EDC)/N-hydroxysuccinimide(NHS). Morphological and chemical analysis of QSH was done using SEM, FTIR, AFM, and protein adsorption test. Thus, porosity, swelling ratio, degradation rate and surface characteristics were evaluated. NIH-3T3 and SaOS-2 cell lines were utilized for 3D cell culture formation. Afterward, 3D spheroids were analyzed for cell viability and proliferation by using AlamarBlue and LiveDead assays, and also cell imaging technics. Results showed that QSH scaffolds did not show any cytotoxic effect on NIH-3T3 and SaOS-2 cells. The optimum results were achieved with 2mg/mL of QSH and 0.03M GTA concentrations; where 76.59µm average pore size, 56.8 fold water holding capacity and at least 80% cell viability was observed. Therefore, it was concluded that QSH has a high potential to promote tissue engineering applications with its injectable texture as a filling material.
Characterization of antioxdant activity and protein functionality in some legume cultivars grown in Turkey
(Izmir Institute of Technology, 2008) Aydemir, Levent Yurdaer; Yemenicioğlu, Ahmet
Turkish chickpeas (4 cultivars) and lentils (6 cultivars) show similar total phenolic contents and free radical scavenging capacities in aqueous extracts ranging between 2869 and 4312 mg gallic acid equivalents/kg legume and 24.42 and 38.20 mmol Trolox equivalents/kg legume, respectively. However, the free radical scavenging capacity of lentil and chickpea protein extracts, range between 110 and 185 mmol Trolox/kg protein and 58 and 144 mmol Trolox/kg protein, respectively, clearly showed the higher free radical scavenging capacity of lentil proteins than chickpea proteins.Protein extracts of chickpeas and lentils showed considerable emulsifying and foaming capacities in almost at the same range, but emulsions and foams formed by chickpea proteins are more stable than those of lentil proteins. The lentil protein extracts are highly soluble and showed poor water absorption and gelling characteristics. In contrast, chickpea protein extracts showed moderate water absorption and gelling capacity.Chickpea protein extracts are also good oil absorbers with almost 1.5 to 2 fold better oil adsorption capacity than lentil protein extracts. Thus, chickpea proteins are suggested as soy and whey protein alternatives for functional proteins used in the food, drug and cosmetics industries. Considering functional properties of proteins for different cultivars, the outstanding Turkish chickpea cultivars are Gökçe and Cevdetbey, while the outstanding Turkish lentil cultivar is Alidayı. Variations in the functional properties of protein suggest the diversity of genes in chickpeas and lentils responsible for these properties. Thus, this study showed the possibility of improving functional properties of chickpeas and lentils by breeding programs.

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