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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Noninvasive in vivo determination of residual strains and stresses(ASME, 2015) N/A; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Donmazov, Samir; Pişkin, Şenol; Pekkan, Kerem; PhD Student; Researcher; Faculty Member; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 148702; 161845Vascular growth and remodeling during embryonic development are associated with blood flow and pressure induced stress distribution, in which residual strains and stresses play a central role. Residual strains are typically measured by performing in vitro tests on the excised vascular tissue. In this paper, we investigated the possibility of estimating residual strains and stresses using physiological pressure-radius data obtained through in vivo noninvasive measurement techniques, such as optical coherence tomography or ultrasound modalities. This analytical approach first tested with in vitro results using experimental data sets for three different arteries such as rabbit carotid artery, rabbit thoracic artery, and human carotid artery based on Fung's pseudostrain energy function and Delfino's exponential strain energy function (SEF). We also examined residual strains and stresses in the human swine iliac artery using the in vivo experimental ultrasound data sets corresponding to the systolic-to-diastolic region only. This allowed computation of the in vivo residual stress information for loading and unloading states separately. Residual strain parameters as well as the material parameters were successfully computed with high accuracy, where the relative errors are introduced in the range of 0-7.5%. Corresponding residual stress distributions demonstrated global errors all in acceptable ranges. A slight discrepancy was observed in the computed reduced axial force. Results of computations performed based on in vivo experimental data obtained from loading and unloading states of the artery exhibited alterations in material properties and residual strain parameters as well. Emerging noninvasive measurement techniques combined with the present analytical approach can be used to estimate residual strains and stresses in vascular tissues as a precursor for growth estimates. This approach is also validated with a finite element model of a general two-layered artery, where the material remodeling states and residual strain generation are investigated.Publication Metadata only Evidence for amino acid snorkeling from a high-resolution, in vivo analysis of FIS1 tail-anchor insertion at the mitochondrial outer membrane(Genetics Society America, 2017) N/A; N/A; N/A; Department of Molecular Biology and Genetics; Keskin, Abdurrahman; Akdoğan, Emel; Dunn, Cory David; Master Student; Master Student; Other; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/AProteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of the Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening of the Fis1p TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs to distinct organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can "snorkel," or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.Publication Metadata only Ultra-efficient and high-quality white light-emitting devices using fluorescent proteins in aqueous medium(Wiley, 2020) N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Sadeghi, Sadra; Melikov, Rustamzhon; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 206349; 130295The transformation of electronics toward “green” and efficient devices is critical for the environmental sustainability and energy future. So far, majority of efficient lighting devices have been realized by artificial optical materials such as rare-earth-elements-doped phosphors, colloidal quantum dots (QDs) and dyes. In this study, red-emitting mScarlet and green-emitting eGFP fluorescent proteins are determined for high-performance white LEDs, expressed in living Escherichia coli and the purified proteins are integrated in their natural aqueous environment onto blue LED chips. The aqueous integration preserved quantum yield levels of the proteins above 70% in the device architecture and facilitated a high luminous efficiency (LE) of 81 lm W−1 with a color rendering index (CRI) of 83, which is the most efficient eco-friendly white LED reported to date. Moreover, the concentration ratio are also optimized of red- and green-emitting proteins and white protein-based LEDs with a maximum CRI of 92 are demonstrated. This study shows that fluorescent proteins hold great promise for the next generation eco-friendly, efficient and high-quality white light sources.Publication Metadata only Ecofriendly and efficient luminescent solar concentrators based on fluorescent proteins(amer Chemical Soc, 2019) N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Sadeghi, Sadra; Melikov, Rustamzhon; Jalali, Houman Bahmani; Karatüm, Onuralp; Srivastava, Shashi Bhushan; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member, Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; 130295In recent years, luminescent solar concentrators (LSCs) have received renewed attention as a versatile platform for large-area, high-efficiency, and low-cost solar energy harvesting. So far, artificial or engineered optical materials, such as rare-earth ions, organic dyes, and colloidal quantum dots (QDs) have been incorporated into LSCs. Incorporation of nontoxic materials into efficient device architectures is critical for environmental sustainability and clean energy production. Here, we demonstrated LSCs based on fluorescent proteins, which are biologically produced, ecofriendly, and edible luminescent biomaterials along with exceptional optical properties. We synthesized mScarlet fluorescent proteins in Escherichia coli expression system, which is the brightest protein with a quantum yield of 61% in red spectral region that matches well with the spectral response of silicon solar cells. Moreover, we integrated fluorescent proteins in an aqueous medium into solar concentrators, which preserved their quantum efficiency in LSCs and separated luminescence and wave-guiding regions due to refractive index contrast for efficient energy harvesting. Solar concentrators based on mScarlet fluorescent proteins achieved an external LSC efficiency of 2.58%, and the integration at high concentrations increased their efficiency approaching to 5%, which may facilitate their use as “luminescent solar curtains” for in-house applications. The liquid-state integration of proteins paves a way toward efficient and “green” solar energy harvesting.