Omer Aydin

Omer Aydin
National Institutes of Health | NIH · NIH Clinical Center (CC)

Ph.D. in Biomedical Engineering

About

28
Publications
5,400
Reads
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406
Citations
Additional affiliations
September 2010 - August 2016
University of Michigan
Position
  • PhD Student
August 2007 - June 2009
Yeditepe University
Position
  • Research Assistant

Publications

Publications (28)
Article
Precise and quick monitoring of key cytometric features such as cell count, cell size, cell morphology, and DNA content is crucial for applications in biotechnology, medical sciences, and cell culture research. Traditionally, image cytometry relies on the use of a hemocytometer accompanied with visual inspection of an operator under a microscope. T...
Article
Full-text available
Bacterial pathogens especially antibiotic-resistant ones are a public health concern worldwide. To oppose the morbidity and mortality associated with them, it is critical to select an appropriate antibiotic by performing a rapid bacterial diagnosis. Using a combination of Raman spectroscopy and deep learning algorithms to identify bacteria is a rap...
Article
Combinational gene and chemo-therapy approach has been investigated for more effective treatment of cancer. In this report, we demonstrated a multifunctional carrier system based on gold nanoparticles (AuNPs) for co-delivery of siRNAs against Bcl-2, an anti-apoptotic gene, and doxorubicin (Dox), a well-known chemotherapy drug, to obtain enhanced tr...
Article
Backgorund Platinum-based chemo therapeutics are main treatment option for the treatment of ovarium cancer. However, development of drug resistance is one of the major issues in chemotherapy. Even targeting a specific pathway may not produce an efficient sensitization to the chemo agent due to various pathways in related to developing resistance ag...
Article
Colistin-resistant Klebsiella pneumoniae (ColR-Kp) causes high mortality rates since colistin is used as the last-line antibiotic against multi-drug resistant Gram-negative bacteria. To reduce infections and mortality rates caused by ColR-Kp fast and reliable detection techniques are vital. In this study, we used a label-free surface-enhanced Raman...
Article
Full-text available
This report describes the development of functionalized polymeric micelles encapsulating a chemotherapeutic agent. The results indicate the ability to achieve selective uptake into different cell populations in metastatic prostate cancer in vitro by appropriate selection of the targeting ligand. This paves the way for administering single or multip...
Article
COVID-19 has caused millions of cases and deaths all over the world since late 2019. Rapid detection of the virus is crucial for controlling its spread through a population. COVID-19 is currently detected by nucleic acid-based tests and serological tests. However, these methods have limitations such as the requirement of high-cost reagents, false n...
Chapter
Full-text available
Nanomaterials have aroused attention in the recent years for their high potential for gene delivery applications. Most of the nanoformulations used in gene delivery are positively charged to carry negatively charged oligonucleotides. However, excessive positively charged carriers are cytotoxic. Therefore, the complexed oligonucleotide/nanoparticles...
Article
Waterborne pathogens (parasites, bacteria) are serious threats to human health. Cryptosporidium parvum is one of the protozoan parasites that can contaminate drinking water and lead to diarrhea in animals and humans. Rapid and reliable detection of these kinds of waterborne pathogens is highly essential. Yet, current detection techniques are limite...
Article
Full-text available
Cancer chemotherapy suffers from drug resistance and side effects of the drugs. Combination therapies have been attracted attention to overcome these limitations of traditional cancer treatments. Recently, increasing in intracellular chemotherapeutic concentration in the presence of ultrasonic waves (US) has been shown in the preclinical stage. In...
Article
Full-text available
Over the past year, the world's attention has focused on combating COVID-19 disease, but the other threat waiting at the door—antimicrobial resistance should not be forgotten. Although making the diagnosis rapidly and accurately is crucial in preventing antibiotic resistance development, bacterial identification techniques include some challenging...
Preprint
Full-text available
Over the past year, the world's attention has focused on combating COVID-19 disease, but the other threat waiting at the door - antimicrobial resistance should not be forgotten. Although making the diagnosis rapidly and accurately is crucial in preventing antibiotic resistance development, bacterial identification techniques include some challengin...
Article
Full-text available
Focused ultrasound (FUS) has shown promise as a non-invasive treatment modality for solid malignancies. FUS targeting to tumors has been shown to initiate pro-inflammatory immune responses within the tumor microenvironment. Pulsed FUS (pFUS) can alter the expression of cytokines, chemokines, trophic factors, cell adhesion molecules, and immune cell...
Article
Full-text available
To combat antibiotic resistance, it is extremely important to select the right antibiotic by performing rapid diagnosis of pathogens. Traditional techniques require complicated sample preparation and time-consuming processes which are not suitable for rapid diagnosis. To address this problem, we used surface-enhanced Raman spectroscopy combined wit...
Article
Full-text available
Non-ablative pulsed focused ultrasound (pFUS) targets non-thermal forces that activate local molecular and cellular immune responses. Optimal parameters to stimulate immunotherapeutic tumor microenvironments (TME) and responses in different tumor types remain uninvestigated. Flank B16 murine melanoma and 4T1 breast tumors received 1 MHz pFUS at 1-8...
Article
We have developed acoustically-activated nanodroplets (NDs) using an amphiphilic triblock copolymer, which self-assembles and encapsulates different perfluorocarbon including perfluoropentane (PFP) and perfluorohexane (PFH). Applying histotripsy waves (i.e. short, high pressure, ultrasound pulses) to solution of PFP- and PFH-NDs generated bubbles c...
Article
Full-text available
We report the synthesis of an amphiphilic triblock copolymer composed of a hydrophilic poly(ethylene glycol) (PEG) block, a central poly(acrylic acid) (PAA) block, and a hydrophobic poly(methyl methacrylate) (PMMA) block using atom transfer radical polymerization technique. We examined the self-assembly of PEG-b-PAA-b-PMMA copolymers in aqueous sol...
Article
Nanodroplet-mediated histotripsy (NMH) is a targeted ablation technique combining histotripsy with nanodroplets that can be selectively delivered to tumor cells. In two previous studies, polymer-encapsulated perfluoropentane nanodroplets were used to generate well-defined ablation similar to that obtained with histotripsy, but at significantly lowe...
Article
Full-text available
Nanodroplet-mediated histotripsy (NMH) is an ultrasound ablation technique combining histotripsy with acoustically sensitive perfluorocarbon (PFC) nanodroplets that can be selectively delivered to tumor cells for targeted tumor ablation. NMH takes advantage of the significantly reduced cavitation threshold of the nanodroplets, allowing for cavitati...
Article
Nanodroplet-mediated histotripsy (NMH) is a targeted ultrasound ablation technique combining histotripsy with nanodroplets that can be selectively delivered to tumor cells for targeted tumor ablation. In a previous study, it was reported that by use of extremely short, high-pressure pulses, histotripsy cavitation bubbles were generated in regions c...
Article
Full-text available
The bimetallic core–shell nanoparticles show unique plasmonic properties and their preparations and characterizations are currently under investigation. A new type of Au core–Ag shell (Au@Ag) nanoparticles is prepared by sandwiching the chemically attached Raman reporter molecules (RRMs) and a 12-base-long oligonucleotide between the 13nm average s...
Article
Full-text available
Surface-enhanced Raman scattering (SERS) is a powerful technique for characterization of biological samples. SERS spectra from healthy brain tissue and tumors are obtained by sudden freezing of tissue in liquid nitrogen and crashing and mixing it with a concentrated silver colloidal suspension. The acquired spectra from tissues show significant spe...
Article
Full-text available
Surface-enhanced Raman scattering (SERS) is proven to be a powerful tool for investigation of biological structures. In this study, tissues obtained from different rat organs are examined using SERS. The tissue samples are crushed with a pestle after sudden freezing in liquid nitrogen and mixed with a concentrated colloidal silver nanoparticle susp...
Article
Mitochondrion is one of the most important organelles in cells with several vital responsibilities. The consequence of a deficiency in the function of mitochondrion could result with the wide range of diseases and disorders. In this study, we investigated the feasibility of utilizing surface-enhanced Raman scattering (SERS) to understand the mode o...
Article
The size influence of 3D silver nanoparticle aggregates on surface-enhanced Raman scattering (SERS) is investigated. Micrometer- and nanometer-sized wells prepared on a polydimethylsiloxane (PDMS) surfaces are filled with cetyltrimethylammonium bromide (CTAB)-coated silver nanoparticles. A concentration of CTAB around its critical micelle concentra...
Conference Paper
Full-text available
The development of an assay for the detection of gene mutations has been attempted based on surface-enhanced Raman scattering (SERS). Using multiplexing property and high sensitivity of SERS technique, the detection of all mutation possibilities on one given spot is achievable. To test the feasibility of approach, SNPs and other types of mutations...

Questions

Questions (2)
Question
We have a sugar-PEG-DOX drug carrier which is water soluble and forms micelle structure whose size is around 60 nm. DOX is bound to PEG block via an enzymaticly cleavable linkage. Our problem is since the polymer forms a micelle structure in aqua system, the enzyme, which will break the bound and leads to releasing of the DOX is not efficient because of limited enzyme can reach the core part of the micelle. Which means the interaction between the enzyme and the linkage is less. My question is how I can increase enzymatic cleavage in our carrier system. I'm open to any suggestion.
Thanks.
Question
I have a question about how to prepare Cabazitaxel drug solution for cell culture experiments, especially to calculate IC50?
The drug is almost insoluble in aqua system. I tried to use 0.5 and 5% DMSO to make it soluble but DMSO acted kind of toxic compound for my cells (PC-3 and C4-2B).
Can you suggest any solvent/medium that can efficiently dissolve the drug?

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