Browsing by Subject "Mass spectrometry"

Now showing 1 - 20 of 22

Open Access
Analysis of polymers using evolved-gas and direct-pyrolysis techniques
(Royal Society of Chemistry, 1994) Fares, M. M.; Yalcin, T.; Hacaloglu, J.; Gungor, A.; Süzer, Şefik
Thermal analysis of polystyrene, poly(p-methylstyrene) and poly(α-methylstyrene) has been carried out using evolved-gas analysis by infrared and mass spectrometry, and direct-pyrolysis analysis by mass spectrometric techniques. Evolved-gas analysis, both by infrared and mass spectrometry, reveals features due mainly to the corresponding monomers or stable, volatile, and low relative molecular mass degradation products. In direct-pyrolysis mass spectrometry, however, primary decomposition products and heavier fragments such as dimers and trimers can also be detected. The ion-temperature profiles of the corresponding monomer ions reveal information about the thermal stability of the polymers.
Open Access
Characterization of degradation products of polyethylene oxide by pyrolysis mass spectrometry
(Pergamon Press, 1994) Fares, M. M.; Hacaloglu, J.; Süzer, Şefik
The techniques of direct and indirect (evolved gas analysis) pyrolysis MS are used to characterize the thermal degradation products of polyethylene oxide. Using direct pyrolysis MS technique the main degradation process is determined to be due to CO and CC scissions yielding fragments characteristic of the polymer. Evolved gas analysis indicates formation of small molecular stable compounds such as C2H5OC2H5, CH3CHO, CO2, CO and C2H4. © 1994.
Open Access
A conducting composite of polypyrrole II. As a gas sensor
(Elsevier, 1995) Selampinar, F.; Toppare, L.; Akbulut, U.; Yalçin, T.; Süzer, Ş.
Pure polypyrrole (PPy) and polypyrrole-polyamide (PPy-PA) composite films were synthesized electrochemically. The gas-sensing ability was investigated for both pure PPy and PPy-PA films. The composite films' response to several gases are better defined and reproducible compared to pristine conducting polymer. Electrochemical behaviour of PPy and PPy-PA electrodes in the presence of pyrrole and pyrrole-free medium is investigated via cyclic voltammetry. Mass spectrometry studies strictly reveal that the composite is completely different to a mechanical mixture. This phenomenon is discussed in comparison to polyaniline-polycarbonate composite. © 1995.
Open Access
Conducting polymer composites of polythiophene with natural and synthetic rubbers
(Elsevier, 1996) Yigit, S.; Hacaloglu, J.; Akbulut, U.; Toppare, L.
Electrochemical synthesis of conducting polymer composites of polythiophene was achieved. Synthetic and natural rubbers were used as the insulating polymer matrices. FT-IR, differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and mass spectrometry (MS) were utilized to characterize the composite blends. The conductivity measurements were done by using a standard four-probe technique. The above-mentioned methods show that the resultant composites have different properties compared to polythiophene due to interaction of the rubbers with electrochemical polymerization of thiophene, whereas the same argument is not valid for the polypyrrole synthesis via the same procedure.
Open Access
Detection of phosphorylation signatures specific to cancer-related PI3-Kinase isoforms p110α and p110β
(2023-01) Sulaiman, Mahnoor
The PI3K signaling pathway is required for many physiological activities, but it is commonly disrupted during cancer formation. The PI3K p110α and βisoforms, encoded by the PIK3CA and PIK3CB genes, are lipid kinases that phosphorylate PIP2 to PIP3 to activate the PI3K pathway. However, the distinct molecular targets of these isoforms have yet to be discovered, making targeted treatment problematic. According to cancer genomics research, the PIK3CA gene is commonly altered in cancers, but the PIK3CB gene is frequently amplified. The clinical usage of Pan-PI3K inhibitors has resulted in significant side effects, prompting the development of isoform-specific inhibitors. However, it has been shown that these drugs trigger alternate signaling systems downstream, leading in resistance to single-agent treatment. Our research intends to uncover distinctive protein-protein interactions of PI3K isoforms, as well as the consequent different phospho-proteomic signatures, which might be crucial determinants of specific cellular activities. This will be accomplished by using isogenic MEF cells that are only dependent on the p110α or p110β isoforms, isoform-specific pharmacological inhibitors BYL-719 and KIN 193, and a high-resolution mass spectrometry-based method to determine the phosphorylation levels of these protein samples. The predictive biomarkers discovered in this study can be utilized to identify patients who will benefit from PI3K-targeted drugs and to better understand the resistance mechanisms that may arise in response to pathway inhibition.
Open Access
The effect of cucurbit[n]uril on the solubility, morphology, and the photophysical properties of nonionic conjugated polymers in an aqueous medium
(2010) Tuncel, D.; Artar, M.; Hanay, S. B.
The effects of cucurbit[n]uril on the dissolution and the photophysical properties of nonionic conjugated polymers in water are described. For this purpose, a fluorine-based polymer, namely, poly[9,9-bis{6(N,N-dimethylamino) hexyl}fluorene-co-2,5-thienylene (PFT) was synthesized and characterized by spectroscopic techniques including 1D and 2D NMR, UV-vis, fluorescent spectroscopy, and matrix-assisted laser desorption mass spectrometry (MALDI-MS). For the first time, it was demonstrated that a nonionic conjugated polymer can be made soluble in water through an inclusion complex formation with CB8. The structure of the complex was elucidated by NMR experiments including 1H and selective 1D-NOESY. This complex emits green and is highly fluorescent with fluorescent quantum yield of 35%. In contrast, CB6 or water-soluble CB7 although they are chemically identical to CB8 do not have any effect on the dissolution and photophysical properties of PFT. By preparing a protonated version of PFT, the optical properties of PFT in methanol, protonated PFT and PFT@CB8 in water have been studied and compared. It was also observed that the morphology of the polymer PFT was affected by the presence of CB8. Thus CB8-assisted self-assembly of polymer chains leads to vesicles formation; these structures were characterized by DLS, AFM, SEM, and TEM fluorescent optical microscopy.
Open Access
Effects of laser ablated silver nanoparticles on Lemna minor
(Elsevier, 2014) Üçüncü, E.; Özkan, A. D.; Kurşungöz, C.; Ülger, Z. E.; Ölmez, T. T.; Tekinay, T.; Ortaç, B.; Tunca E.
Open Access
Electrospinning of functional poly(methyl methacrylate) nanofibers containing cyclodextrin-menthol inclusion complexes
(Institute of Physics Publishing, 2009) Uyar, Tamer; Nur, Y.; Hacaloglu, J.; Besenbacher, F.
Electrospinning of nanofibers with cyclodextrin inclusion complexes (CD-ICs) is particularly attractive since distinct properties can be obtained by combining the nanofibers with specific functions of the CD-ICs. Here we report on the electrospinning of poly(methyl methacrylate) (PMMA) nanofibers containing cyclodextrin-menthol inclusion complexes (CD-menthol-ICs). These CD-menthol-IC functionalized nanofibers were developed with the purpose of producing functional nanofibers that contain fragrances/flavors with high temperature stability, and menthol was used as a model fragrance/flavor material. The PMMA nanofibers were electrospun with CD-menthol-ICs using three type of CD: α-CD, β-CD, and γ-CD. Direct pyrolysis mass spectrometry (DP-MS) studies showed that the thermal evaporation of menthol occurred over a very high and a broad temperature range (100-355 °C) for PMMA/CDmenthol-IC nanowebs, demonstrating the complexation of menthol with the CD cavity and its high temperature stability. Furthermore, as the size of CD cavity increased in the order α-CD<β-CD<γ-CD, the thermal evolution of menthol shifted to higher temperatures, suggesting that the strength of interaction between menthol and the CD cavity is in the order γ-CD>β-CD>α-CD. © 2009 IOP Publishing Ltd.
Open Access
Induction of triacylglycerol production in Chlamydomonas reinhardtii: comparative analysis of different element regimes
(Elsevier, 2014) Çakmak, Z. E.; Ölmez, T. T.; Çakmak, T.; Menemen, Y.; Tekinay, T.
In this study, impacts of different element absence (nitrogen, sulfur, phosphorus and magnesium) and supplementation (nitrogen and zinc) on element uptake and triacylglycerol production was followed in wild type Chlamydomonas reinhardtii CC-124 strain. Macro- and microelement composition of C. reinhardtii greatly differed under element regimes studied. In particular, heavy metal quotas of the microalgae increased strikingly under zinc supplementation. Growth was suppressed, cell biovolume, carbohydrate, total neutral lipid and triacylglycerol levels increased when microalgae were incubated under these element regimes. Most of the intracellular space was occupied by lipid bodies under all nutrient starvations, as observed by confocal microscopy and transmission electron micrographs. Results suggest that sulfur, magnesium and phosphorus deprivations are superior to nitrogen deprivation for the induction triacylglycerol production in C. reinhardtii. On the other hand, FAME profiles of the nitrogen, sulfur and phosphorus deprived cells were found to meet the requirements of international standards for biodiesel.
Open Access
Inertial imaging with nanomechanical systems
(Nature Publishing Group, 2015) Hanay, M. S.; Kelber, S. I.; O'Connell, C. D.; Mulvaney, P.; Sader, J. E.; Roukes, M. L.
Mass sensing with nanoelectromechanical systems has advanced significantly during the last decade. With nanoelectromechanical systems sensors it is now possible to carry out ultrasensitive detection of gaseous analytes, to achieve atomic-scale mass resolution and to perform mass spectrometry on single proteins. Here, we demonstrate that the spatial distribution of mass within an individual analyte can be imaged - in real time and at the molecular scale - when it adsorbs onto a nanomechanical resonator. Each single-molecule adsorption event induces discrete, time-correlated perturbations to all modal frequencies of the device. We show that by continuously monitoring a multiplicity of vibrational modes, the spatial moments of mass distribution can be deduced for individual analytes, one-by-one, as they adsorb. We validate this method for inertial imaging, using both experimental measurements of multimode frequency shifts and numerical simulations, to analyse the inertial mass, position of adsorption and the size and shape of individual analytes. Unlike conventional imaging, the minimum analyte size detectable through nanomechanical inertial imaging is not limited by wavelength-dependent diffraction phenomena. Instead, frequency fluctuation processes determine the ultimate attainable resolution. Advanced nanoelectromechanical devices appear capable of resolving molecular-scale analytes.
Open Access
Mass spectrometry using nanomechanical systems: beyond the point-mass approximation
(American Chemical Society, 2018) Sader, J. E.; Hanay, Selim; Neumann, A. P.; Roukes, M. L.
The mass measurement of single molecules, in real time, is performed routinely using resonant nanomechanical devices. This approach models the molecules as point particles. A recent development now allows the spatial extent (and, indeed, image) of the adsorbate to be characterized using multimode measurements (Hanay, M. S., Nature Nanotechnol., 10, 2015, pp.
Open Access
Non-covalent functionalized SWNTs as delivery agents for novel Bodipy-based potential PDT sensitizers
(2009) Erbas, S.; Gorgulu, A.; Kocakusakogullari, M.; Akkaya, E. U.
Pyrenyl-functionalized distyryl-Bodipy sensitizer attached non-covalently to SWNTs was shown to generate singlet oxygen when excited at 660 nm with a red LED array; this work emphasizes the potential of SWNT as a viable alternative carrier of bioactive agents, including photodynamic therapy sensitizers. © 2009 The Royal Society of Chemistry.
Open Access
Nonlinear nanomechanical mass spectrometry at the single-nanoparticle level
(American Chemical Society, 2019) Yüksel, Mert; Orhan, Ezgi; Yanık, C.; Arı, Atakan B.; Demir, A.; Hanay, Mehmet Selim
Nanoelectromechanical systems (NEMS) have emerged as a promising technology for performing the mass spectrometry of large biomolecules and nanoparticles. As nanoscale objects land on NEMS sensors one by one, they induce resolvable shifts in the resonance frequency of the sensor proportional to their weight. The operational regime of NEMS sensors is often limited by the onset of nonlinearity, beyond which the highly sensitive schemes based on frequency tracking by phase-locked loops cannot be readily used. Here, we develop a measurement architecture with which to operate at the nonlinear regime and measure frequency shifts induced by analytes in a rapid and sensitive manner. We used this architecture to individually characterize the mass of gold nanoparticles and verified the results by performing independent measurements of the same nanoparticles based on linear mass sensing. Once the feasibility of the technique is established, we have obtained the mass spectrum of a 20 nm gold nanoparticle sample by individually recording about 500 single-particle events using two modes working sequentially in the nonlinear regime. The technique obtained here can be used for thin nanomechanical structures that possess a limited dynamic range.
Open Access
Phosphoproteomic analysis of class IA P110β isoform-specific signal transducers upon PI3K pathway activation
(2023-08) Daloğlu, Beril
PI3K pathway activation is a common event observed in various human cancers. As it regulates cell proliferation, migration and metabolism, it has been widely targeted for anticancer therapies and alteration of drug resistance. Studies focusing on PI3K Class IA isoform-specific inhibition has become critical to achieve alternative targeted treatment methods. Although previous findings show that Class IA isoforms differ in their routes of activation, the downstream targets specific to the isoforms have not been fully profiled yet. This study focuses on the phosphoproteomic analysis of p110 isoform-specific downstream molecules upon PI3K pathway activation. We have created a doxycycline-inducible system in Mouse Embryonic Fibroblasts (MEFs) to express wildtype PIK3CB gene encoding p110β or its catalytic and helical domain over-activating mutants, E1051K and N553S. By immunoblotting, the changes in downstream phosphorylation events were analyzed for MEF p110β mutants or for MEF p110β WT cells upon mitogenic PI3K stimulation. These results were collaborated with the comparative phosphoproteomic data obtained from LC-MS/MS Mass Spectrometry analysis. Our findings show that upon short-term stimulation of the PI3K pathway, proteins associated with transcriptional regulation, cytoskeletal rearrangement, cellular signalling, migration and metabolism are differentially phosphorylated. After longer stimulations on the other hand, proteins involved in cell cycle progression, phosphatase activity, nucleocytoplasmic transport and RNA metabolism become more prominent in the comparative phosphoproteome. Similar to early response proteins in β WT cells, the phosphoproteome of β E1051K cells were associated with cytoskeletal rearrangement and cellular migration. Aligning with the morphological changes observed, proteins involved in anatomical structure regulation were found. Additionally, some tumour suppressors and oncogene proteins were found among the differentially regulated phosphoproteins. On the other hand, the phosphoproteome of β N553S cells were enriched for functions of RNA metabolism, nuclear import and apoptotic regulation. Proteins involved in structural organization and microtubule assembly were also observed. 37 kDa Akt substrate Poly(rC) Binding Protein 1 (Pcbp1) was found as a common differentially phosphorylated protein in the phosphoproteomes of mutant and WT p110β expressing cells. It is an RNA-binding protein associated with metastasis and EMT, and has a critical role in gene expression by coordinating RNA stability and processing. As our results have shown that p110β isoform has a major role in cytoskeletal reorganization, cell migration and transcriptional regulation, studying the regulation of p110β-Pcbp1 axis can pave the way to understand the mechanisms of increased tumour progression in p110β-dependent cells.
Open Access
Photocatalytic conversion of nitric oxide on titanium dioxide: cryotrapping of reaction products for online monitoring by mass spectrometry
(American Chemical Society, 2016) Lu, W.; Olaitan, A. D.; Brantley, M. R.; Zekavat, B.; Erdogan, D. A.; Ozensoy, E.; Solouki, T.
Details of coupling a catalytic reaction chamber to a liquid nitrogen-cooled cryofocuser/triple quadrupole mass spectrometer for online monitoring of nitric oxide (NO) photocatalytic reaction products are presented. Cryogenic trapping of catalytic reaction products, via cryofocusing prior to mass spectrometry analysis, allows unambiguous characterization of nitrous oxide (N2O) and nitrogen oxide species (i.e., NO and nitrogen dioxide (NO2)) at low concentrations. Results are presented, indicating that the major photocatalytic reaction product of NO in the presence of titanium dioxide (TiO2) P25 and pure anatase catalysts when exposed to ultraviolet (UV) light (at a wavelength of 365 nm) is N2O. However, in the presence of rutile-rich TiO2 catalyst and UV light, the conversion of NO to N2O was less than 5% of that observed with the P25 or pure anatase TiO2 catalysts.
Open Access
Production and structural characterization of biosurfactant produced by newly isolated staphylococcus xylosus STF1 from petroleum contaminated soil
(Elsevier BV, 2015) Keskin, N. O. S.; Han, D.; Ozkan A.D.; Angun, P.; Umu, O. C. O.; Tekinay, T.
Petroleum-contaminated soil was used to isolate and characterize biosurfactant producing bacteria. The strain could produce higher amount of biosurfactant in medium supplemented with motor oil as sole source of carbon and energy. A new biosurfactant producing bacterium, designated as Staphylococcus xylosus STF1 based on morphological, physiological, biochemical tests and 16S rRNA gene sequencing. The isolated bacterium was first screened for the ability to produce biosurfactant. Partial sequence of STF1 strain of 16S rDNA gene was highly similar to those of various members of the family Staphylococcaceae. Biochemical characterizations including FT-IR, Raman spectroscopy and Mass spectroscopy studies suggested the biosurfactant to be lipopeptide. Study also confirmed that the cell free supernatant exhibited high emulsifying activity against the different hydrocarbons. Moreover, the partially purified biosurfactant exhibited antimicrobial activity by inhibiting the growth of several bacterial species. The strain could be a potential candidate for the production of polypeptide biosurfactant which could be useful in a variety of biotechnological and industrial processes, particularly in the food and oil industry. © 2015 Elsevier B.V.
Open Access
Profiling the interactome of STK10 by using proximity-based biotinylation
(2023-05) Carus, Yağmur Öykü
Breast cancer accounts for a quarter of all newly diagnosed cancer cases globally in women. It is also the primary cause of death in female cancer patients. In 2020, it was responsible for 15% of all cancer-related deaths in women. The PI3K pathway is the most commonly deregulated pathway in breast cancer. As a result, numerous inhibitors for druggable targets within the pathway have been developed. Unfortunately, drug resistance is frequently observed after treatment with these inhibitors. The mechanisms behind this resistance are widely studied. AKT has been known to be the kinase responsible for transmitting the signal to downstream targets. However, new studies suggested there can be AKT-independent kinases relaying the signal to downstream targets causing PI3K inhibitor drug resistance. Previously, our group hypothesized that they could find an AKT-independent protein that confers resistance to PI3K inhibition. Their bioinformatical analyses identified STK10 (Serine-Threonine Kinase 10) as a possible druggable target for PI3K pathway inhibitor resistance in an AKT-independent manner. They performed wet lab experiments to show STK10’s impact on PI3K inhibitor resistance in breast cancer. They showed STK10 knock-down sensitizing resistant breast cancer cells to PI3K inhibitor. Although their experiments supported the hypothesis of STK10 affecting the PI3K inhibitor resistance of breast cancer cells, they could not identify the molecular mechanisms behind this interaction. In this study, by using APEX2 proximity-based biotinylation followed by mass spectrometry, we profiled STK10’s interactome. We aimed to understand how STK10 contributes to the progression of breast cancer and the development of resistance to treatment. Our bioinformatics analyses indicated possible interaction between STK10 and the candidate proteins we obtained from our mass spectrometry analysis. Immunofluorescence and Co-IP experiments supported some of the putative interactions we discovered. The proteins discovered near STK10 were primarily linked to the reorganization of the cytoskeleton, which is encouraging since STK10 is recognized for its involvement in cell migration through the phosphorylation of ERM proteins. Based on our observations, it is possible to hypothesize that STK10 is influencing the cytoskeletal reorganization in breast cancer cells. However, further experiments are needed to be done to understand the molecular mechanisms behind STK10’s possible functions in breast cancer. These experiments could lead to uncovering the role of STK10 in PI3K inhibitor resistance and help us to identify new therapeutic options to battle breast cancer.
Open Access
Sensing and characterization of single nanoparticles by vacuum-free nanoelectromechanical systems with an integrated polymeric lens
(2021-08) Erdoğan, Ramazan Tufan
Machines in the nanoscale dimension had the opportunity to become a top-notch choice to detect and characterize nanoparticles thanks to the rapid progress in micro-nano fabrication. Sensors that can detect and identify nanoparticles al-lowed the analysis of the physics on the scale of nanometers. In the last decade, nano-electromechanical systems are evolved with the integration of electronics to the mechanical nano dimensional structures to sense the mass of particles. Their small form factor, high sensitivity to mass changes, and compatibility with the microchip fabrication process placed NEMS in a position to be an excellent can-didate for sensing applications. In contrast, high sensitivity that is coming from their minuscule size of active area for mass detection comes with the cost of hav-ing minimal eﬃciency in capturing the nanoparticles in concern. Moreover, the need for vacuum equipment for the transportation of the nanoparticles conﬁned NEMS-MS applications to the laboratories. Here, we resolved these problems by integrating a polymeric lens on top of the NEMS sensors in order to transport and direct the incoming nanoparticles, utilizing the electric ﬁeld only, towards the minuscule active detection area; with exploiting change of the electric ﬁeld in between nanoparticle source and NEMS, due to the accumulating surface charges over the polymeric lens. Therefore, we executed mass sensing measurements and obtained the mass spectrum of the 40 nm diameter gold nanoparticles and 100 nm diameter polystyrene nanoparticles without diﬀerential vacuum equipment, with a rapid analysis time and high capture eﬃciency.
Open Access
Sequence-specific self-sorting of the binding sites of a ditopic guest by cucurbituril homologues and subsequent formation of a hetero[4]pseudorotaxane
(2009) Celtek, G.; Artar, M.; Scherman, O. A.; Tuncel, D.
Ties us together: The selectivity and recognition behavior of cucurbit[n]uril (CB[n]) homologues (n = 6,7,8) towards a ditopic guest containing two distinct binding sites is explored. CB6, CB7, and CB8 recognize and self-sort the binding sites according to their size, shape, and chemical nature. In the presence of both CB6 and CB8 a hetero[4]pseudorotaxane is formed. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.
Open Access
Single nanoparticle sensing with nanoelectromechanical resonators operating at nonlinear regime
(2019-08) Yüksel, Mert
Machines working at the nanoscale dimensions o er an important technological opportunity for healthcare and biomedical screening. State-of-the-art nanomachines are usually operated at small displacements, since engineering tools for their control at large vibration amplitudes have so far been absent. Nanoelectromechanical Systems (NEMS) have emerged as a promising technology for performing the mass spectrometry of large biomolecules and nanoparticles. Nanoparticles constitute an important family in the nanotechnology toolbox, because they indicate potential pollutions early on, or can be designed to act as drug carriers for cancer therapy. As nanoscale objects land on NEMS sensor one by one, they induce resolvable shifts in the resonance frequency of the sensor proportional to their weight. The operational regime of NEMS sensors is often limited by the onset-of-nonlinearity, beyond which the highly sensitive schemes based on frequency tracking by phase-locked loops cannot be readily used. Here, we develop a measurement architecture to operate at the nonlinear regime and measure frequency shifts induced by analytes in a rapid and sensitive manner. We used this architecture to individually characterize the mass of gold nanoparticles and veri ed the results by performing independent measurements of the same nanoparticles based on linear mass sensing. Once the feasibility of the technique is established, we have obtained the mass spectrum of a 20 nm gold nanoparticle sample by individually recording about ve hundred single particle events using two modes working sequentially in the nonlinear regime. The technique obtained here can be used for thin nanomechanical structures which possess a limited dynamic range.