A searchable listing of most recent publications using IRIS Kinetics technologies.
You can search for any words contained in the title or abstract.
1.
Chatterjee, Rusha; Scheidt, Rebecca; Hilton, Michael; Yu, Tiffany; Unlu, M. Selim; Giblin, Jay; Dupuis, Julia
Interferometric reflectance imaging sensor for biothreat detection (IRIS-BD) Proceedings
SPIE proceedings, 2025, (Event: SPIE Defense + Commercial Sensing, 2025, Orlando, Florida, United States).
Abstract | Links | BibTeX | Tags:
@proceedings{nokey,
title = {Interferometric reflectance imaging sensor for biothreat detection (IRIS-BD)},
author = {Rusha Chatterjee and Rebecca Scheidt and Michael Hilton and Tiffany Yu and M. Selim Unlu and Jay Giblin and Julia Dupuis},
url = {https://doi.org/10.1117/12.3053489},
year = {2025},
date = {2025-05-28},
abstract = {There is a critical need for sensors that can provide rapid detection and identification of biological threats in the field. Currently established approaches (cell cultures, polymerase chain reactions, mass spectrometry) are time consuming, susceptible to contamination, or not amenable to field use. Physical Sciences Inc. in collaboration with iRiS Kinetics is developing a compact, portable and fieldable sensor for the rapid detection and presumptive identification of biothreats. The technology—termed Interferometric Reflectance Imaging Sensor for Biothreat Detection (IRIS-BD)—is a microfluidics-based lab-on-chip immunoassay and can screen for the detection and presumptive identification of bacterial, viral and toxin threats. The system employs three key components—an antibody conjugated to single stranded deoxyribonucleic acid (DNA), a complementary DNA functionalized sensing chip that interferometrically enhances the imaging contrast of captured particles, and an optical chip reader. The sensor can screen for up to 5 agents in a single assay and provide a detection and presumptive identification decision in <2 hours. The interferometric imaging optical approach is capable of detecting a single captured biothreat particle on the sensing chip. This ability gives IRIS-BD the potential to have comparable specificity to lateral flow immunoassays but with 50–1000× improved detection capabilities. A description of the sensor architecture and initial results on testing against biothreat simulants is presented here.},
howpublished = {SPIE proceedings},
note = {Event: SPIE Defense + Commercial Sensing, 2025, Orlando, Florida, United States},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
There is a critical need for sensors that can provide rapid detection and identification of biological threats in the field. Currently established approaches (cell cultures, polymerase chain reactions, mass spectrometry) are time consuming, susceptible to contamination, or not amenable to field use. Physical Sciences Inc. in collaboration with iRiS Kinetics is developing a compact, portable and fieldable sensor for the rapid detection and presumptive identification of biothreats. The technology—termed Interferometric Reflectance Imaging Sensor for Biothreat Detection (IRIS-BD)—is a microfluidics-based lab-on-chip immunoassay and can screen for the detection and presumptive identification of bacterial, viral and toxin threats. The system employs three key components—an antibody conjugated to single stranded deoxyribonucleic acid (DNA), a complementary DNA functionalized sensing chip that interferometrically enhances the imaging contrast of captured particles, and an optical chip reader. The sensor can screen for up to 5 agents in a single assay and provide a detection and presumptive identification decision in <2 hours. The interferometric imaging optical approach is capable of detecting a single captured biothreat particle on the sensing chip. This ability gives IRIS-BD the potential to have comparable specificity to lateral flow immunoassays but with 50–1000× improved detection capabilities. A description of the sensor architecture and initial results on testing against biothreat simulants is presented here.
2.
Bakhshpour-Yücel, Monireh; Aljayyousi, Nawal; Osman, Bilgen; Ünlü, Nese Lortlar; Denizli, Adil; Ünlü, M. Selim
Nanomaterial-Based Sensing Systems to Detect Neuropharmaceutical Compounds and Neurotransmitters Journal Article
In: Sensors, vol. 25, iss. 11, pp. 3256, 2025.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Nanomaterial-Based Sensing Systems to Detect Neuropharmaceutical Compounds and Neurotransmitters},
author = {Monireh Bakhshpour-Yücel and Nawal Aljayyousi and Bilgen Osman and Nese Lortlar Ünlü and Adil Denizli and M. Selim Ünlü},
url = {https://doi.org/10.3390/s25113256},
year = {2025},
date = {2025-05-22},
journal = {Sensors},
volume = {25},
issue = {11},
pages = {3256},
abstract = {This review explores the application of nanomaterial-based sensing systems for precisely detecting neuropharmaceutical compounds and neurotransmitters, delving into the connections between nanotechnology and neuropharmacology. Nanotechnology appears as a promising solution for many significant challenges posed by the complexities of the brain’s biochemical nature. Using nanoscale materials, scientists have created novel sensors with high selectivity, sensitivity, and adaptability. Developing neuropharmaceutical compounds and monitoring their side effects on our neurological system raised the need for these nanomaterial-based sensors. In this review, we demonstrate the effectiveness of these technologies in real-time neuroactive compound detection and monitoring by illuminating the underlying principles through an examination of significant studies and recent developments. This review also highlights collaborative efforts at the intersection of nanotechnology and neuropharmacology and their direct and indirect effects on the understanding and controlling several neurological disorders. This review covers both sensors under research and those already applied in vivo or clinical monitoring of drug side effects.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This review explores the application of nanomaterial-based sensing systems for precisely detecting neuropharmaceutical compounds and neurotransmitters, delving into the connections between nanotechnology and neuropharmacology. Nanotechnology appears as a promising solution for many significant challenges posed by the complexities of the brain’s biochemical nature. Using nanoscale materials, scientists have created novel sensors with high selectivity, sensitivity, and adaptability. Developing neuropharmaceutical compounds and monitoring their side effects on our neurological system raised the need for these nanomaterial-based sensors. In this review, we demonstrate the effectiveness of these technologies in real-time neuroactive compound detection and monitoring by illuminating the underlying principles through an examination of significant studies and recent developments. This review also highlights collaborative efforts at the intersection of nanotechnology and neuropharmacology and their direct and indirect effects on the understanding and controlling several neurological disorders. This review covers both sensors under research and those already applied in vivo or clinical monitoring of drug side effects.
3.
Aslan, Mete; Seymour, Elif; Brickner, Howard; Clark, Alex E.; Celebi, Iris; Townsend, Michael B.; Satheshkumar, Panayampalli S.; Riley, Megan; Carlin, Aaron F.; Ünlü, M. Selim; Ray, Partha
A label-free optical biosensor-based point-of-care test for the rapid detection of Monkeypox virus Journal Article
In: Biosensors and Bioelectronics, vol. 269, 2025.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {A label-free optical biosensor-based point-of-care test for the rapid detection of Monkeypox virus},
author = {Mete Aslan and Elif Seymour and Howard Brickner and Alex E. Clark and Iris Celebi and Michael B. Townsend and Panayampalli S. Satheshkumar and Megan Riley and Aaron F. Carlin and M. Selim Ünlü and Partha Ray },
url = {https://doi.org/10.1016/j.bios.2024.116932},
year = {2025},
date = {2025-02-01},
urldate = {2025-02-01},
journal = {Biosensors and Bioelectronics},
volume = {269},
abstract = {Diagnostic approaches that combine the high sensitivity and specificity of laboratory-based digital detection with the ease of use and affordability of point-of-care (POC) technologies could revolutionize disease diagnostics. This is especially true in infectious disease diagnostics, where rapid and accurate pathogen detection is critical to curbing the spread of disease. We have pioneered an innovative label-free digital detection platform that utilizes Interferometric Reflectance Imaging Sensor (IRIS) technology. IRIS leverages light interference from an optically transparent thin film, eliminating the need for complex optical resonances to enhance the signal by harnessing light interference and the power of signal averaging in shot-noise-limited operation In our latest work, we have further improved our previous 'Single-Particle' IRIS (SP-IRIS) technology by allowing the construction of the optical signature of target nanoparticles (whole virus) from a single image. This new platform, 'Pixel-Diversity' IRIS (PD-IRIS), eliminated the need for z-scan acquisition, required in SP-IRIS, a time-consuming and expensive process, and made our technology more applicable to POC settings. Using PD-IRIS, we quantitatively detected the Monkeypox virus (MPXV), the etiological agent for Monkeypox (Mpox) infection. MPXV was captured by anti-A29 monoclonal antibody (mAb 69-126-3) on Protein G spots on the sensor chips and were detected at a limit-of-detection (LOD) - of 200 PFU/mL (∼3.3 aM). PD-IRIS was superior to the laboratory-based ELISA (LOD - 1800 PFU/mL) used as a comparator. The specificity of PD-IRIS in MPXV detection was demonstrated using Herpes simplex virus, type 1 (HSV-1), and Cowpox virus (CPXV). This work establishes the effectiveness of PD-IRIS and opens possibilities for its advancement in clinical diagnostics of Mpox at POC. Moreover, PD-IRIS is a modular technology that can be adapted for the multiplex detection of pathogens for which high-affinity ligands are available that can bind their surface antigens to capture them on the sensor surface.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Diagnostic approaches that combine the high sensitivity and specificity of laboratory-based digital detection with the ease of use and affordability of point-of-care (POC) technologies could revolutionize disease diagnostics. This is especially true in infectious disease diagnostics, where rapid and accurate pathogen detection is critical to curbing the spread of disease. We have pioneered an innovative label-free digital detection platform that utilizes Interferometric Reflectance Imaging Sensor (IRIS) technology. IRIS leverages light interference from an optically transparent thin film, eliminating the need for complex optical resonances to enhance the signal by harnessing light interference and the power of signal averaging in shot-noise-limited operation In our latest work, we have further improved our previous 'Single-Particle' IRIS (SP-IRIS) technology by allowing the construction of the optical signature of target nanoparticles (whole virus) from a single image. This new platform, 'Pixel-Diversity' IRIS (PD-IRIS), eliminated the need for z-scan acquisition, required in SP-IRIS, a time-consuming and expensive process, and made our technology more applicable to POC settings. Using PD-IRIS, we quantitatively detected the Monkeypox virus (MPXV), the etiological agent for Monkeypox (Mpox) infection. MPXV was captured by anti-A29 monoclonal antibody (mAb 69-126-3) on Protein G spots on the sensor chips and were detected at a limit-of-detection (LOD) - of 200 PFU/mL (∼3.3 aM). PD-IRIS was superior to the laboratory-based ELISA (LOD - 1800 PFU/mL) used as a comparator. The specificity of PD-IRIS in MPXV detection was demonstrated using Herpes simplex virus, type 1 (HSV-1), and Cowpox virus (CPXV). This work establishes the effectiveness of PD-IRIS and opens possibilities for its advancement in clinical diagnostics of Mpox at POC. Moreover, PD-IRIS is a modular technology that can be adapted for the multiplex detection of pathogens for which high-affinity ligands are available that can bind their surface antigens to capture them on the sensor surface.
4.
Brambilla, Dario; Panico, Federica; Unlu, M Selim; Chiari, Marcella
Sequential separation and profiling of extracellular vesicles using antibody-aptamer conjugates Journal Article
In: Sensors and Actuators B: Chemical, vol. 424, 2025.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Sequential separation and profiling of extracellular vesicles using antibody-aptamer conjugates},
author = {Dario Brambilla and Federica Panico and M Selim Unlu and Marcella Chiari},
url = {https://doi.org/10.1016/j.snb.2024.136939},
year = {2025},
date = {2025-02-01},
urldate = {2023-11-29},
journal = {Sensors and Actuators B: Chemical},
volume = {424},
abstract = {Extracellular vesicles (EVs) are membrane-bound vesicles secreted by cells, exhibiting diverse compositions reflective of their cellular origin. With significant potential as biomarkers for liquid biopsies, EV research has led to various isolation techniques. However, a consensus on the optimal strategy remains elusive. Immunoprecipitation, selectively capturing EVs based on surface markers, is promising but hindered by cost, low yields, and potential damage during release. In this study, we propose an innovative Antibody-Aptamer Conjugate: a three-component separation reagent for the separation of EVs. Combining an EV-specific antibody, a streptavidin-binding aptamer, and a unique barcode DNA sequence, this conjugate serves dual roles, facilitating both EV separation and subsequent multiplexed analysis. We detail the development and validation of the Antibody-Aptamer Conjugate, demonstrating its efficacy in isolating intact EVs from complex samples. The unique barcode DNA sequence enables high-throughput analysis on a DNA microarray chip, addressing limitations of existing methodologies. This approach offers a valid and cost-effective alternative for selective EV isolation and analysis, with implications for diagnostic and therapeutic advancements in liquid biopsy applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Extracellular vesicles (EVs) are membrane-bound vesicles secreted by cells, exhibiting diverse compositions reflective of their cellular origin. With significant potential as biomarkers for liquid biopsies, EV research has led to various isolation techniques. However, a consensus on the optimal strategy remains elusive. Immunoprecipitation, selectively capturing EVs based on surface markers, is promising but hindered by cost, low yields, and potential damage during release. In this study, we propose an innovative Antibody-Aptamer Conjugate: a three-component separation reagent for the separation of EVs. Combining an EV-specific antibody, a streptavidin-binding aptamer, and a unique barcode DNA sequence, this conjugate serves dual roles, facilitating both EV separation and subsequent multiplexed analysis. We detail the development and validation of the Antibody-Aptamer Conjugate, demonstrating its efficacy in isolating intact EVs from complex samples. The unique barcode DNA sequence enables high-throughput analysis on a DNA microarray chip, addressing limitations of existing methodologies. This approach offers a valid and cost-effective alternative for selective EV isolation and analysis, with implications for diagnostic and therapeutic advancements in liquid biopsy applications.
5.
Selim, M; Aslan, Mete; Gray, Alexander; Packard, Logan; Giorgetta, Caeden; Bigio, Irving
Impact of uniform illumination in widefield microscopy and mesoscopy: An efficient flat-field imaging solution Journal Article
In: Optica Open, 2025.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Impact of uniform illumination in widefield microscopy and mesoscopy: An efficient flat-field imaging solution},
author = {M Selim and Mete Aslan and Alexander Gray and Logan Packard and Caeden Giorgetta and Irving Bigio},
url = {https://preprints.opticaopen.org/ndownloader/files/51641945},
year = {2025},
date = {2025-01-01},
journal = {Optica Open},
abstract = {Illumination uniformity is critical for widefield optical microscopy, especially for
high-throughput and accurate quantitative imaging of biological specimens. While traditional
Köhler illumination improves uniformity, it often fails to deliver homogeneous intensity across
large fields of view. Existing optical and computational correction techniques remain
inadequate for a broad range of quantitative imaging applications. Here, we implement a novel
illumination device that we call the “effective uniform color-light integration device”
(EUCLID), quantifying improvements in two widefield imaging modalities that require
uniform illumination. For both imaging modalities, we demonstrate significantly improved
precision of quantitative measurements compared to traditional Köhler illumination. The
EUCLID device, which can also provide uniform spectral mixing, can be readily adapted to
many other widefield imaging modalities to enhance imaging accuracy and reliability, with low
cost and ease of implementation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Illumination uniformity is critical for widefield optical microscopy, especially for
high-throughput and accurate quantitative imaging of biological specimens. While traditional
Köhler illumination improves uniformity, it often fails to deliver homogeneous intensity across
large fields of view. Existing optical and computational correction techniques remain
inadequate for a broad range of quantitative imaging applications. Here, we implement a novel
illumination device that we call the “effective uniform color-light integration device”
(EUCLID), quantifying improvements in two widefield imaging modalities that require
uniform illumination. For both imaging modalities, we demonstrate significantly improved
precision of quantitative measurements compared to traditional Köhler illumination. The
EUCLID device, which can also provide uniform spectral mixing, can be readily adapted to
many other widefield imaging modalities to enhance imaging accuracy and reliability, with low
cost and ease of implementation.
high-throughput and accurate quantitative imaging of biological specimens. While traditional
Köhler illumination improves uniformity, it often fails to deliver homogeneous intensity across
large fields of view. Existing optical and computational correction techniques remain
inadequate for a broad range of quantitative imaging applications. Here, we implement a novel
illumination device that we call the “effective uniform color-light integration device”
(EUCLID), quantifying improvements in two widefield imaging modalities that require
uniform illumination. For both imaging modalities, we demonstrate significantly improved
precision of quantitative measurements compared to traditional Köhler illumination. The
EUCLID device, which can also provide uniform spectral mixing, can be readily adapted to
many other widefield imaging modalities to enhance imaging accuracy and reliability, with low
cost and ease of implementation.
6.
Ünlü, Elisa Chiodi Monireh Bakhshpour-Yucel Nese Lortlar
Characterization of Receptor Binding Affinity for Vascular Endothelial Growth Factor with Interferometric Imaging Sensor Journal Article
In: Biosensors, vol. 14, iss. 7, pp. 315, 2024.
@article{nokey,
title = {Characterization of Receptor Binding Affinity for Vascular Endothelial Growth Factor with Interferometric Imaging Sensor},
author = {Elisa Chiodi Monireh Bakhshpour-Yucel Nese Lortlar Ünlü},
year = {2024},
date = {2024-06-24},
journal = {Biosensors},
volume = {14},
issue = {7},
pages = {315},
abstract = {Wet Age-related macular degeneration (AMD) is the leading cause of vision loss in industrialized nations, often resulting in blindness. Biologics, therapeutic agents derived from biological sources, have been effective in AMD, albeit at a high cost. Due to the high cost of AMD treatment, it is critical to determine the binding affinity of biologics to ensure their efficacy and make quantitative comparisons between different drugs. This study evaluates the in vitro VEGF binding affinity of two drugs used for treating wet AMD, monoclonal antibody-based bevacizumab and fusion protein-based aflibercept, performing quantitative binding measurements on an Interferometric Reflectance Imaging Sensor (IRIS) system. Both biologics can inhibit Vascular Endothelial Growth Factor (VEGF). For comparison, the therapeutic molecules were immobilized on to the same support in a microarray format, and their real-time binding interactions with recombinant human VEGF (rhVEGF) were measured using an IRIS. The results indicated that aflibercept exhibited a higher binding affinity to VEGF than bevacizumab, consistent with previous studies using ELISA and SPR. The IRIS system’s innovative and cost-effective features, such as silicon-based semiconductor chips for enhanced signal detection and multiplexed analysis capability, offer new prospects in sensor technologies. These attributes make IRISs a promising tool for future applications in the development of therapeutic agents, specifically biologics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wet Age-related macular degeneration (AMD) is the leading cause of vision loss in industrialized nations, often resulting in blindness. Biologics, therapeutic agents derived from biological sources, have been effective in AMD, albeit at a high cost. Due to the high cost of AMD treatment, it is critical to determine the binding affinity of biologics to ensure their efficacy and make quantitative comparisons between different drugs. This study evaluates the in vitro VEGF binding affinity of two drugs used for treating wet AMD, monoclonal antibody-based bevacizumab and fusion protein-based aflibercept, performing quantitative binding measurements on an Interferometric Reflectance Imaging Sensor (IRIS) system. Both biologics can inhibit Vascular Endothelial Growth Factor (VEGF). For comparison, the therapeutic molecules were immobilized on to the same support in a microarray format, and their real-time binding interactions with recombinant human VEGF (rhVEGF) were measured using an IRIS. The results indicated that aflibercept exhibited a higher binding affinity to VEGF than bevacizumab, consistent with previous studies using ELISA and SPR. The IRIS system’s innovative and cost-effective features, such as silicon-based semiconductor chips for enhanced signal detection and multiplexed analysis capability, offer new prospects in sensor technologies. These attributes make IRISs a promising tool for future applications in the development of therapeutic agents, specifically biologics.
7.
Bakhshpour-Yucel, Iris Çelebi Sinem Diken-Gür Monireh
Interferometric reflectance imaging sensor for diagnosis and therapy Book Chapter
In: Academic Press, 2024.
@inbook{nokey,
title = {Interferometric reflectance imaging sensor for diagnosis and therapy},
author = {Iris Çelebi Sinem Diken-Gür Monireh Bakhshpour-Yucel},
year = {2024},
date = {2024-01-01},
publisher = {Academic Press},
series = {Biophysics At the Nanoscale},
abstract = {This chapter introduces the working principles and applications of interferometric reflectance imaging sensors (IRISs), which proved its success as a highly sensitive detection tool in diagnosis. Briefly, the surface chemistry of low-cost Si–SiO2 IRIS chips, probe molecules placement on the chip surface with microarray technology, data collection after molecular interactions, image analysis, and data processing steps are described in this section. Moreover, IRIS, which offers label-free and multiplex assay opportunities, has two different models depending on the camera features. Measurement of bioaccumulation depending on the binding of analyte on the chip surface is realized by low magnification IRIS model. On the other hand, with a high-magnification version of IRIS model, a single particle with nanosized can be detected and also visualized individually.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
This chapter introduces the working principles and applications of interferometric reflectance imaging sensors (IRISs), which proved its success as a highly sensitive detection tool in diagnosis. Briefly, the surface chemistry of low-cost Si–SiO2 IRIS chips, probe molecules placement on the chip surface with microarray technology, data collection after molecular interactions, image analysis, and data processing steps are described in this section. Moreover, IRIS, which offers label-free and multiplex assay opportunities, has two different models depending on the camera features. Measurement of bioaccumulation depending on the binding of analyte on the chip surface is realized by low magnification IRIS model. On the other hand, with a high-magnification version of IRIS model, a single particle with nanosized can be detected and also visualized individually.
8.
Xia, Haonan Zong Zhongyue Guo Qing
Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy Journal Article
In: Nature Communications, vol. 14, iss. 1, pp. 6655, 2023.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy},
author = {Haonan Zong Zhongyue Guo Qing Xia},
url = {https://www.nature.com/articles/s41467-023-42439-4},
year = {2023},
date = {2023-10-20},
journal = {Nature Communications},
volume = {14},
issue = {1},
pages = {6655},
abstract = {Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella ...},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella ...
9.
Celebi, M Selim Ünlü Mete Aslan Iris
A spatially uniform illumination source for widefield multi-spectral optical microscopy Journal Article
In: Plos one, vol. 18, iss. 10, pp. e0286988, 2023.
@article{nokey,
title = {A spatially uniform illumination source for widefield multi-spectral optical microscopy},
author = {M Selim Ünlü Mete Aslan Iris Celebi},
year = {2023},
date = {2023-10-18},
journal = {Plos one},
volume = {18},
issue = {10},
pages = {e0286988},
abstract = {Illumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ≈ 1% across a wide field-of-view.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Illumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ≈ 1% across a wide field-of-view.
10.
Aslan, M Selim Unlu Iris Celebi Mete
Polarization-Diversity Interferometric Imaging for Digital Biodetection Conference
Imaging Systems and Applications, vol. IW5E. 4, Optica Publishing Group, 2023.
@conference{nokey,
title = {Polarization-Diversity Interferometric Imaging for Digital Biodetection},
author = {M Selim Unlu Iris Celebi Mete Aslan},
year = {2023},
date = {2023-08-14},
booktitle = {Imaging Systems and Applications},
volume = {IW5E. 4},
publisher = {Optica Publishing Group},
abstract = {We present a new digital biomolecule detection technique based on interferometric imaging of plasmonic gold nanorod labels. Post-processing of polarization camera readout allows for effective background rejection in a single snapshot.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
We present a new digital biomolecule detection technique based on interferometric imaging of plasmonic gold nanorod labels. Post-processing of polarization camera readout allows for effective background rejection in a single snapshot.
11.
Seymour, Sinem Diken Gür Fulya Ekiz Kanik Elif
Solid-phase optical sensing techniques for sensitive virus detection Journal Article
In: Sensors, vol. 23, iss. 11, pp. 5018, 2023.
@article{nokey,
title = {Solid-phase optical sensing techniques for sensitive virus detection},
author = {Sinem Diken Gür Fulya Ekiz Kanik Elif Seymour},
year = {2023},
date = {2023-05-24},
journal = {Sensors},
volume = {23},
issue = {11},
pages = {5018},
abstract = {Viral infections can pose a major threat to public health by causing serious illness, leading to pandemics, and burdening healthcare systems. The global spread of such infections causes disruptions to every aspect of life including business, education, and social life. Fast and accurate diagnosis of viral infections has significant implications for saving lives, preventing the spread of the diseases, and minimizing social and economic damages. Polymerase chain reaction (PCR)-based techniques are commonly used to detect viruses in the clinic. However, PCR has several drawbacks, as highlighted during the recent COVID-19 pandemic, such as long processing times and the requirement for sophisticated laboratory instruments. Therefore, there is an urgent need for fast and accurate techniques for virus detection. For this purpose, a variety of biosensor systems are being developed to provide rapid, sensitive, and high-throughput viral diagnostic platforms, enabling quick diagnosis and efficient control of the virus’s spread. Optical devices, in particular, are of great interest due to their advantages such as high sensitivity and direct readout. The current review discusses solid-phase optical sensing techniques for virus detection, including fluorescence-based sensors, surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS), optical resonators, and interferometry-based platforms. Then, we focus on an interferometric biosensor developed by our group, the single-particle interferometric reflectance imaging sensor (SP-IRIS), which has the capability to visualize single nanoparticles, to demonstrate its application for digital virus ...},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Viral infections can pose a major threat to public health by causing serious illness, leading to pandemics, and burdening healthcare systems. The global spread of such infections causes disruptions to every aspect of life including business, education, and social life. Fast and accurate diagnosis of viral infections has significant implications for saving lives, preventing the spread of the diseases, and minimizing social and economic damages. Polymerase chain reaction (PCR)-based techniques are commonly used to detect viruses in the clinic. However, PCR has several drawbacks, as highlighted during the recent COVID-19 pandemic, such as long processing times and the requirement for sophisticated laboratory instruments. Therefore, there is an urgent need for fast and accurate techniques for virus detection. For this purpose, a variety of biosensor systems are being developed to provide rapid, sensitive, and high-throughput viral diagnostic platforms, enabling quick diagnosis and efficient control of the virus’s spread. Optical devices, in particular, are of great interest due to their advantages such as high sensitivity and direct readout. The current review discusses solid-phase optical sensing techniques for virus detection, including fluorescence-based sensors, surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS), optical resonators, and interferometry-based platforms. Then, we focus on an interferometric biosensor developed by our group, the single-particle interferometric reflectance imaging sensor (SP-IRIS), which has the capability to visualize single nanoparticles, to demonstrate its application for digital virus ...
12.
Bakhshpour-Yucel, Elif Seymour Sinem Diken Gür Monireh
Highly-sensitive, label-free detection of microorganisms and viruses via interferometric reflectance imaging sensor Journal Article
In: Micromachines, vol. 14, iss. 2, pp. 281, 2023.
@article{nokey,
title = {Highly-sensitive, label-free detection of microorganisms and viruses via interferometric reflectance imaging sensor},
author = {Elif Seymour Sinem Diken Gür Monireh Bakhshpour-Yucel},
year = {2023},
date = {2023-01-21},
journal = {Micromachines},
volume = {14},
issue = {2},
pages = {281},
abstract = {Pathogenic microorganisms and viruses can easily transfer from one host to another and cause disease in humans. The determination of these pathogens in a time- and cost-effective way is an extreme challenge for researchers. Rapid and label-free detection of pathogenic microorganisms and viruses is critical in ensuring rapid and appropriate treatment. Sensor technologies have shown considerable advancements in viral diagnostics, demonstrating their great potential for being fast and sensitive detection platforms. In this review, we present a summary of the use of an interferometric reflectance imaging sensor (IRIS) for the detection of microorganisms. We highlight low magnification modality of IRIS as an ensemble biomolecular mass measurement technique and high magnification modality for the digital detection of individual nanoparticles and viruses. We discuss the two different modalities of IRIS and their applications in the sensitive detection of microorganisms and viruses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pathogenic microorganisms and viruses can easily transfer from one host to another and cause disease in humans. The determination of these pathogens in a time- and cost-effective way is an extreme challenge for researchers. Rapid and label-free detection of pathogenic microorganisms and viruses is critical in ensuring rapid and appropriate treatment. Sensor technologies have shown considerable advancements in viral diagnostics, demonstrating their great potential for being fast and sensitive detection platforms. In this review, we present a summary of the use of an interferometric reflectance imaging sensor (IRIS) for the detection of microorganisms. We highlight low magnification modality of IRIS as an ensemble biomolecular mass measurement technique and high magnification modality for the digital detection of individual nanoparticles and viruses. We discuss the two different modalities of IRIS and their applications in the sensitive detection of microorganisms and viruses.
13.
Seymour, Elif; Ünlü, M. Selim; Connor, John H
A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies Journal Article
In: Scientific Reports, vol. 13, iss. 1, pp. 1, 2023.
Abstract | Links | BibTeX | Tags:
@article{nokeyb,
title = {A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies},
author = {Elif Seymour and M. Selim Ünlü and John H Connor},
url = {https://www.researchsquare.com/article/rs-1898923/v1},
doi = {doi.org/10.21203/rs.3.rs-1898923/v1},
year = {2023},
date = {2023-01-16},
urldate = {2022-08-03},
journal = {Scientific Reports},
volume = {13},
issue = {1},
pages = {1},
abstract = {Monoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases.
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Monoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases.
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails
14.
Celebi, Iris; Aslan, Mete; Ünlü, M. Selim
A spatially uniform illumination source for widefield multi-spectral optical microscopy Journal Article Forthcoming
In: Physics Optics, Forthcoming.
Abstract | Links | BibTeX | Tags:
@article{Celebi2022,
title = {A spatially uniform illumination source for widefield multi-spectral optical microscopy},
author = {Iris Celebi and Mete Aslan and M. Selim Ünlü},
url = {https://arxiv.org/abs/2212.06216
},
doi = {https://doi.org/10.48550/arXiv.2212.06216},
year = {2022},
date = {2022-12-12},
journal = {Physics Optics},
abstract = {llumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ~1% across a wide field-of-view.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
llumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ~1% across a wide field-of-view.
15.
Kanik, Fulya Ekiz; Celebi, Iris; Sevenler, Derin; Tanriverdi, Kahraman; Ünlü, Nese Lortlar; Freedman, Jane E.; Ünlü, M. Selim
Attomolar sensitivity microRNA detection using real‑time digital microarrays Journal Article
In: Scientific Reports, vol. 2022, no. 12, pp. 16220, 2022.
Abstract | Links | BibTeX | Tags: Oligo
@article{nokey,
title = {Attomolar sensitivity microRNA detection using real‑time digital microarrays},
author = {Fulya Ekiz Kanik and Iris Celebi and Derin Sevenler and Kahraman Tanriverdi and Nese Lortlar Ünlü and Jane E. Freedman and M. Selim Ünlü},
url = {https://axivend.com/wp-content/uploads/2022/09/Attomolar-sensitivity-microRNA-detection.pdf},
doi = {10.1038/s41598-022-19912-z},
year = {2022},
date = {2022-09-27},
urldate = {2022-09-27},
journal = {Scientific Reports},
volume = {2022},
number = {12},
pages = {16220},
abstract = {MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA‑451a (miR‑451) and miRNA‑223‑3p (miR‑223). We demonstrated improvements in sensitivity in comparison to traditional end‑point assays that employ capture on solid phase support, by implementing real‑time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low‑abundance biomarkers in the presence
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.},
keywords = {Oligo},
pubstate = {published},
tppubtype = {article}
}
MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA‑451a (miR‑451) and miRNA‑223‑3p (miR‑223). We demonstrated improvements in sensitivity in comparison to traditional end‑point assays that employ capture on solid phase support, by implementing real‑time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low‑abundance biomarkers in the presence
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
16.
Kanik, Fulya Ekiz; Celebi, Iris; Sevenler, Derin; Tanriverdi, Kahraman; Ünlü, Nese Lortlar; Freedman, Jane E.; Ünlü, M. Selim
Attomolar sensitivity microRNA detection using real‑time digital microarrays Journal Article
In: Scientific Reports, vol. 2022, iss. 2, no. 12, pp. 16220, 2022.
Abstract | Links | BibTeX | Tags: Oligo
@article{nokey,
title = {Attomolar sensitivity microRNA detection using real‑time digital microarrays},
author = {Fulya Ekiz Kanik and Iris Celebi and Derin Sevenler and Kahraman Tanriverdi and Nese Lortlar Ünlü and Jane E. Freedman and M. Selim Ünlü},
url = {https://mhg912.p3cdn1.secureserver.net/wp-content/uploads/2022/09/Attomolar-sensitivity-microRNA-detection.pdf},
doi = {10.1038/s41598-022-19912-z},
year = {2022},
date = {2022-09-27},
urldate = {2022-09-27},
booktitle = {Imaging Systems and Applications},
journal = {Scientific Reports},
volume = {2022},
number = {12},
issue = {2},
pages = {16220},
publisher = {Optica Publishing Group},
series = {Biophysics At the Nanoscale},
abstract = {MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA‑451a (miR‑451) and miRNA‑223‑3p (miR‑223). We demonstrated improvements in sensitivity in comparison to traditional end‑point assays that employ capture on solid phase support, by implementing real‑time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low‑abundance biomarkers in the presence
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.},
howpublished = {https://chemrxiv.org/engage/chemrxiv/article-details/6565fc1829a13c4d4730f055},
keywords = {Oligo},
pubstate = {published},
tppubtype = {article}
}
MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA‑451a (miR‑451) and miRNA‑223‑3p (miR‑223). We demonstrated improvements in sensitivity in comparison to traditional end‑point assays that employ capture on solid phase support, by implementing real‑time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low‑abundance biomarkers in the presence
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
of low‑affinity but high‑abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to ∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
17.
Seymour, Elif; Ünlü, M. Selim; Connor, John H
A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies Journal Article Forthcoming
In: https://www.researchsquare.com/article/rs-1898923/v1, Forthcoming.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies},
author = {Elif Seymour and M. Selim Ünlü and John H Connor},
url = {https://www.researchsquare.com/article/rs-1898923/v1
},
doi = {doi.org/10.21203/rs.3.rs-1898923/v1},
year = {2022},
date = {2022-08-03},
urldate = {2022-08-03},
journal = {https://www.researchsquare.com/article/rs-1898923/v1},
abstract = {Monoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases.
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Monoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases.
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails
Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30
mAbs against Ebola and Lassa viruses (EBOV and LASV) to find out the ideal capture antibodies for
whole virus detection using recombinant VSV (rVSV) models expressing surface glycoproteins of EBOV
and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the
antibody epitopes on the glycoprotein structure. mAbs that bind to mucin-like domain or glycan cap of
the EBOV surface glycoprotein show the highest signal on SP-IRIS, followed by mAbs that target the GP1-
GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV
infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best
performance on SP-IRIS. This antibody binds to a unique region on the surface glycoprotein compared to
other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and
rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb
cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher
efficacy compared to other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do
not compete with each other for binding to EBOV GP. In fact, binding of 13C6 enhances the binding of
2G4 and 4G7 antibodies. SP-IRIS is a versatile tool that can provide high-throughput screening of mAbs,
multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails
18.
Bakhshpour, M; Chiodi, E; Celebi, I; Saylan, Y; Ünlü, NL; Ünlü, MS; Denizli, A
Sensitive and real-time detection of IgG using interferometric reflecting imaging sensor system Journal Article
In: Biosensors and Bioelectronics, vol. 201, pp. 113961, 2022.
Abstract | Links | BibTeX | Tags: Protein
@article{nokeyc,
title = {Sensitive and real-time detection of IgG using interferometric reflecting imaging sensor system},
author = {M Bakhshpour and E Chiodi and I Celebi and Y Saylan and NL Ünlü and MS Ünlü and A Denizli},
doi = {https://doi.org/10.1016/j.bios.2021.113961},
year = {2022},
date = {2022-04-01},
urldate = {2022-04-01},
journal = {Biosensors and Bioelectronics},
volume = {201},
pages = {113961},
abstract = {Considering the limitations of well-known traditional detection techniques, innovative research studies have focused on the development of new sensors to offer label-free, highly sensitive, real-time, low-cost, and rapid detection for biomolecular interactions. In this study, we demonstrate immunoglobulin G (IgG) detection in aqueous solutions by using real-time and label-free kinetic measurements of the Interferometric Reflectance Imaging Sensor (IRIS) system. By performing kinetic characterization experiments, the sensor's performance is comprehensively evaluated and a high correlation coefficient value (>0.94) is obtained in the IgG concentration range of 1–50 μg/mL with a low detection limit (0.25 μg/mL or 1.67 nM). Moreover, the highly sensitive imaging system ensures accurate quantification and reliable validation of recorded binding events, offering new perspectives in terms of direct biomarker detection for clinical applications.},
keywords = {Protein},
pubstate = {published},
tppubtype = {article}
}
Considering the limitations of well-known traditional detection techniques, innovative research studies have focused on the development of new sensors to offer label-free, highly sensitive, real-time, low-cost, and rapid detection for biomolecular interactions. In this study, we demonstrate immunoglobulin G (IgG) detection in aqueous solutions by using real-time and label-free kinetic measurements of the Interferometric Reflectance Imaging Sensor (IRIS) system. By performing kinetic characterization experiments, the sensor's performance is comprehensively evaluated and a high correlation coefficient value (>0.94) is obtained in the IgG concentration range of 1–50 μg/mL with a low detection limit (0.25 μg/mL or 1.67 nM). Moreover, the highly sensitive imaging system ensures accurate quantification and reliable validation of recorded binding events, offering new perspectives in terms of direct biomarker detection for clinical applications.
19.
Chiodi, E; Marn, AM; Bakhshpour, M; Ünlü, N Lortlar Ünlü MS
The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors Journal Article
In: Polymers, vol. 14, iss. 2, pp. 241, 2022.
Abstract | Links | BibTeX | Tags: Oligo, Protein
@article{nokeyd,
title = {The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors},
author = {E Chiodi and AM Marn and M Bakhshpour and N Lortlar Ünlü MS Ünlü},
editor = {Ick-Soo Kim},
url = {https://www.mdpi.com/2073-4360/14/2/241},
doi = {https://doi.org/10.3390/polym14020241},
year = {2022},
date = {2022-01-07},
urldate = {2022-01-07},
journal = {Polymers},
volume = {14},
issue = {2},
pages = {241},
abstract = {The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches},
keywords = {Oligo, Protein},
pubstate = {published},
tppubtype = {article}
}
The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches
20.
Chiodi, E; Marn, AM; Bakhshpour, M; ans MS Ünlü, N Lortlar Ünlü
The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors Journal Article
In: Polymers, vol. 14, iss. 2, pp. 241, 2022.
Abstract | Links | BibTeX | Tags: Oligo, Protein
@article{nokey,
title = {The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors},
author = {E Chiodi and AM Marn and M Bakhshpour and N Lortlar Ünlü ans MS Ünlü},
editor = {Ick-Soo Kim},
url = {https://www.mdpi.com/2073-4360/14/2/241},
doi = {https://doi.org/10.3390/polym14020241},
year = {2022},
date = {2022-01-07},
urldate = {2022-01-07},
journal = {Polymers},
volume = {14},
issue = {2},
pages = {241},
abstract = {The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches},
keywords = {Oligo, Protein},
pubstate = {published},
tppubtype = {article}
}
The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches
