Monitoring of inflammatory response to cancer immunotherapies.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15199-e15199 ◽  
Author(s):  
Qimin Quan ◽  
John Geanacopoulos ◽  
Joshua Ritchey ◽  
Mark Clenow ◽  
Joe Wilkinson ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Single Molecule ◽  
Dynamic Range ◽  
Color Change ◽  
High Sensitivity ◽  
Test Methods ◽  
Label Free ◽  
Cell Therapies ◽  
Color Changes ◽  
Cmos Compatible

e15199 Background: Inflammation observed in response to some monoclonal antibody drugs and adaptive T-Cell therapies has become a major issue in cancer immunotherapy. Prognostic monitoring of the inflammatory response requires simultaneous measurement of multiple cytokines at widely divergent concentrations. At present, no analytical method, known to us, can provide large dynamic range (> 6 logs), high sensitivity (< 1pg/ml) and high multiplex in a single test. Methods: The NanoMosaic platform is a cytokine quantification technology powered by silicon nanoneedle biosensors that are densely integrated on a plate and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a label-free biosensor, functionalized with capture antibodies. Each analyte specific sensing area consists a total of ~23k nanoneedles divided into a digital region (~20k nanoneedles) and an analog region (~3k nanoneedles), combined to cover the entire range of inflammatory biomarkers from 0.1pg/ml to 1ug/ml. Results: We demonstrated that the digital nanoneedles achieve the single molecule sensitivity. Therefore, at ultra-low concentrations when antigens that are captured by the nanoneedles follow Poisson statistics, the number of antigens can be quantitated by counting the presence or absence of color changes of individual nanoneedles in a binary fashion. As the protein concentrations increase, the binding events increase accordingly and achieve saturation when all nanoneedles capture more than one protein. Above the digital saturation concentration, an adjacent section of analog nanoneedles perform quantitative analysis based on the level of color change, thus providing a wider dynamic range up to 1ug/ml. Each single analyte area, including both digital and analog sensors, is less than 500um. Therefore, high level multiplex can be achieved by duplicating the detection sensor in a microarray format without loss of sensitivity and dynamic range. Conclusions: The CMOS-compatible NanoMosaic technology provides the cost-effectiveness, sensitivity, dynamic range and multiplexing capacity required to fully integrate patient immune response into therapeutic development and decision making.

Proteome-wide biomarker quantification and target screening.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15205-e15205
Author(s):  
Qimin Quan ◽  
John Geanacopoulos ◽  
Joshua Ritchey ◽  
Mark Clenow ◽  
Joe Wilkinson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Molecule ◽  
Dynamic Range ◽  
Color Change ◽  
Label Free ◽  
Development Programs ◽  
Color Changes ◽  
Scattering Spectrum ◽  
Proteome Level ◽  
Target Screening

e15205 Background: Existing drug development programs are represented by only a few hundred protein targets. A large subset of the ~20,000 proteins encoded by the human genome remain undiscovered. Proteome-wide “druggability” screening may lead to new targets for therapeutics. Methods: The NanoMosaic platform is a digital immunoassay technology that achieves sub-pg/ml level sensitivity, whole-proteome level multiplexing capability, and 7 logs of dynamic range. The platform overcomes the sensitivity and dynamic range limitations of traditional protein arrays and mass spectrometry. Results: The NanoMosaic technology is powered by silicon nanoneedle biosensors that are densely integrated on a plate and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a label-free biosensor, functionalized with capture antibodies. Its scattering spectrum changes when an antigen binds to its surface. Each analyte specific sensing area consists a total of ~23k nanoneedles divided into a digital region (~20k nanoneedles) and an analog region (~3k nanoneedles). The digital nanoneedles provide the single molecule sensitivity. Therefore, at ultra-low concentration when antigens that are captured by the nanoneedles follow Poisson statistics, the number of antigens can be quantitated by counting the presence or absence of color changes of individual nanoneedles in a binary fashion. As the protein concentrations increase, the binding event counts increase accordingly and achieve saturation when all nanoneedles capture more than one protein. Above the digital saturation concentration, an adjacent section of analog nanoneedles perform quantitative analysis based on the level of color change, thus providing a wider dynamic range up to 1ug/ml. Ultrahigh level multiplex can be achieved by parallelizing the detection in a microarray format without loss of the sensitivity and dynamic range. A 20,000-plex proteome-wide study can be achieved with a total of 5 billion nanoneedles on a ~70mm by 70mm chip. Conclusions: In conclusion, proteome-wide biomarker quantification and target discovery can be performed on the NanoMosaic platform at higher sensitivity, wider dynamic range, lower cost and higher throughput than is currently possible by mass spectrometry or traditional immunoassays.

MosaicNeedles: A tool for multi-omic liquid biopsy sensitivity and specificity enhancement.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15019-e15019
Author(s):  
Qimin Quan ◽  
Joe Wilkinson ◽  
Joshua Ritchey ◽  
Alaina Kaiser ◽  
John Geanacopoulos ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Molecule ◽  
Liquid Biopsy ◽  
Dynamic Range ◽  
Color Change ◽  
Protein Detection ◽  
Target Sequence ◽  
Label Free ◽  
Protein Biomarkers ◽  
Oncology Research

e15019 Background: Liquid biopsy has evolved to be an important method complementary to tissue biopsy. It is not only non-invasive, but also has the potential to detect cancer in its earliest stages and monitor patients in remission. The integration of proteomics into liquid biopsy may transform the molecular diagnostics of cancer and accelerate basic and clinical oncology research. A recent study showed that adding just 8 protein biomarkers to a panel of circulating DNA biomarkers increased the diagnostic accuracy up to 98% sensitivity and 99% specificity. Proteomics also bridges the gaps of functional information lost due to post-transcriptional and post-translational modifications in the genomic approach. However, the proteogenomic approach normally requires the use of multiple different assay technologies and laboratory workflows, including mass spectrometry. Methods: NanoMosaic’s Tessie platform employs a densely integrated nanoneedle sensor array (thus named MosaicNeedles) which can be used to detect both nucleic acids and proteins in a single assay process with reduced workflow complexity, without the need for mass spectrometry. Results: The NanoMosaic platform is a label-free, digital, single molecule counting technology using nanoneedles. It achieves sub-pg/ml (̃fM) level sensitivity with 7 logs of dynamic range. An array of nanoneedles is densely integrated and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a single molecule biosensor that is functionalized with capture probes. The capture probe can be either an antibody for protein detection or an oligonucleotide with a specific target sequence to a DNA fragment, mRNA, or miRNA of interest. The scattering spectrum of each nanoneedle changes when an analyte binds to its surface. At low abundance, analytes that are captured can be quantitated by counting the presence or absence of a color change on each individual nanoneedle in a binary fashion. As an analyte concentration increases the binding events increase accordingly and achieve saturation. In this range, an analog analysis on the spectrum shift will be performed, thus providing a wider dynamic range, up to 7 logs. Ultrahigh level multiplex can be achieved by parallelizing each analyte specific sensing area without loss of sensitivity or dynamic range. A 10,000-plex study can be achieved with a total of 2.5 billion nanoneedles on a 50mm by 50mm consumable. In this consumable, a 2,000-plex proteome and 8,000 cell-free DNA fragments can be detected. Conclusions: In conclusion, a full proteogenomic quantification can be performed on the NanoMosaic platform in one reaction, with higher sensitivity, lower cost and higher throughput than is currently possible by traditional methods. In addition, the high-plexibility of the NanoMosaic platform allows the discovery of new biomarkers across the whole proteome without the need for mass spectrometry.

Interim Report on THE LIGHTFASTNESS CORRELATION PROJECT

2011 ◽  
Vol 1319 ◽  
Author(s):  
Mark D. Gottsegen
Keyword(s):  
Western Europe ◽  
Color Change ◽  
Light Exposure ◽  
Extended Period ◽  
Test Sample ◽  
Test Methods ◽  
Light Sources ◽  
Initial Development ◽  
Color Changes ◽  
Single Number

ABSTRACTThis paper describes the five-year Lightfastness Correlation Project that I am conducting in sixteen institutions in the US and Western Europe, with the support of the Samuel H. Kress Foundation.Dr. Robert L. Feller, a scientist at the National Gallery of Art, published several papers in the 1970s in which he speculated that a certain duration of time could be correlated, in a general way, to the color changes noted in the Blue Wool Textile Fading Cards. Museums use the cards as inexpensive dosimeters, put somewhere in a gallery along with the art. Enough is known about their behavior to have confidence in their ability to indicate when it is time to remove an object from exhibition.The Blue Wools are also used in two Standards developed by ASTM International’s Subcommittee D01.57 on Artists’ Paints and Related Materials. ASTM D 5383 and ASTM D 5398 are simple lightfastness test methods. In them, the Blue Wool cards are exposed to natural daylight along with any colored material, and are used to tell the artist when it’s time to stop the test and as a rating device.Another ASTM Standard from D01.57, ASTM D4303, uses instruments to control the accumulated amount of natural daylight, or simulated daylight in a xenon arc light exposure machine. It also uses a spectrophotometer to calculate the color change that can occur in a test sample, expressed in CIE L*a*b*. There is also a standard formula for calculating color change that results in a single number, expressed as Delta E, or ∆E.The ∆E number is used by ASTM D01.57 to assign lightfastness ratings to artists’ coloring materials covered by its Specifications for various products. Initial development of the ASTM methods began in 1977; we have 33 years of data that confirms the worth of the methods used in our testing.What is the relationship between the results of Blue Wool testing and the results using D01.57’s technical ∆Es? This is a fundamental question we have yet to thoroughly examine. We have begun to work on the problem, using accelerated natural and artificial light sources as in ASTM D 4303. But no one has ever tried to compare the results of these two test methods in a museum environment, over an extended period of real time.“The Lightfastness Correlation Project” ends in August 2011, and a final scientific report will be submitted to the sponsor, The Samuel H. Kress Foundation, in September 2011.

scholarly journals Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

2015 ◽  
Vol 112 (32) ◽  
pp. E4354-E4363 ◽  
Author(s):  
Fatih Inci ◽  
Chiara Filippini ◽  
Murat Baday ◽  
Mehmet Ozgun Ozen ◽  
Semih Calamak ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Point Of Care ◽  
Medical Diagnostics ◽  
Clinical Samples ◽  
Label Free ◽  
Protein Biomarkers ◽  
Electrical Field ◽  
Color Changes ◽  
Sensing Platform ◽  
Broad Dynamic Range

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes.

scholarly journals Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Nano Research ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 328-333 ◽  
Author(s):  
Andrea Spitaleri ◽  
Denis Garoli ◽  
Moritz Schütte ◽  
Hans Lehrach ◽  
Walter Rocchia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Molecule ◽  
Dynamic Range ◽  
Protein Sequencing ◽  
High Fidelity ◽  
Label Free ◽  
Therapeutic Approaches ◽  
Highly Sensitive ◽  
Dynamics Simulations ◽  
Structure Of Proteins

AbstractSingle molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the “shape” of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

scholarly journals Single-Molecule Detection of DNA in a Nanochannel by High-Field Strength-Assisted Electrical Impedance Spectroscopy

Micromachines ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 189 ◽  
Author(s):  
Porpin Pungetmongkol ◽  
Takatoki Yamamoto
Keyword(s):  
Single Molecule ◽  
High Intensity ◽  
High Sensitivity ◽  
Electrical Impedance Spectroscopy ◽  
Random Coil ◽  
Label Free ◽  
Electrode Gap ◽  
Label Free Detection ◽  
Intensity Field ◽  
Nanogap Electrodes

Many researchers have fabricated micro and nanofluidic devices incorporating optical, chemical, and electrical detection systems with the aim of achieving on-chip analysis of macromolecules. The present study demonstrates a label-free detection of DNA using a nanofluidic device based on impedance measurements that is both sensitive and simple to operate. Using this device, the electrophoresis and dielectrophoresis effect on DNA conformation and the length dependence were examined. A low alternating voltage was applied to the nanogap electrodes to generate a high intensity field (>0.5 MV/m) under non-faradaic conditions. In addition, a 100 nm thick gold electrode was completely embedded in the substrate to allow direct measurements of a solution containing the sample passing through the gap, without any surface modification required. The high intensity field in this device produced a dielectrophoretic force that stretched the DNA molecule across the electrode gap at a specific frequency, based on back and forth movements between the electrodes with the DNA in a random coil conformation. The characteristics of 100 bp, 500 bp, 1 kbp, 5 kbp, 10 kbp, and 48 kbp λ DNA associated with various conformations were quantitatively analyzed with high resolution (on the femtomolar level). The sensitivity of this system was found to be more than about 10 orders of magnitude higher than that obtained from conventional linear alternating current (AC) impedance for the analysis of bio-polymers. This new high-sensitivity process is expected to be advantageous with regard to the study of complex macromolecules and nanoparticles.

scholarly journals Conformational pathway provides unique sensitivity to a synaptic mGluR

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Chris H. Habrian ◽  
Joshua Levitz ◽  
Vojtech Vyklicky ◽  
Zhu Fu ◽  
Adam Hoagland ◽  
...  
Keyword(s):  
Single Molecule ◽  
Metabotropic Glutamate Receptors ◽  
Dynamic Range ◽  
High Sensitivity ◽  
G Protein Coupled Receptors ◽  
Metabotropic Glutamate ◽  
Single Molecule Fret ◽  
Broad Dynamic Range ◽  
Maximal Activation ◽  
G Protein Coupled

AbstractMetabotropic glutamate receptors (mGluRs) are dimeric G-protein–coupled receptors that operate at synapses. Macroscopic and single molecule FRET to monitor structural rearrangements in the ligand binding domain (LBD) of the mGluR7/7 homodimer revealed it to have an apparent affinity ~4000-fold lower than other mGluRs and a maximal activation of only ~10%, seemingly too low for activation at synapses. However, mGluR7 heterodimerizes, and we find it to associate with mGluR2 in the hippocampus. Strikingly, the mGluR2/7 heterodimer has high affinity and efficacy. mGluR2/7 shows cooperativity in which an unliganded subunit greatly enhances activation by agonist bound to its heteromeric partner, and a unique conformational pathway to activation, in which mGluR2/7 partially activates in the Apo state, even when its LBDs are held open by antagonist. High sensitivity and an unusually broad dynamic range should enable mGluR2/7 to respond to both glutamate transients from nearby release and spillover from distant synapses.

Top-down Fabricated Polysilicon Nanoribbon Biosensor Chips for Cancer Diagnosis

2013 ◽  
Vol 1569 ◽  
pp. 213-218
Author(s):  
Hsiao-Kang Chang ◽  
Xiaoli Wang ◽  
Noppadol Aroonyadet ◽  
Rui Zhang ◽  
Yan Song ◽  
...  
Keyword(s):  
Dynamic Range ◽  
High Sensitivity ◽  
Cmos Process ◽  
Label Free ◽  
Top Down ◽  
Wide Dynamic Range ◽  
Critical Dimensions ◽  
Require Time ◽  
Significant Research ◽  
Conventional Photolithography

ABSTRACTNanobiosensors have drawn significant research interest in recent years owing to the advantages of label-free, electrical detection. However, nanobiosensors fabricated by bottom-up process are limited in terms of yield and device uniformity due to the challenges in assembly. Nanobiosensors fabricated by top-down process, on the other hand, exhibit better uniformity but require time and costly processes and materials to achieve the critical dimensions required for high sensitivity. In this report, we introduce a top-down nanobiosensor based on polysilicon nanoribbon. The polysilicon nanoribbon devices can be fabricated by conventional photolithography with only materials and equipments used in the standard CMOS process, thus resulting in great time and cost efficiency, as well as scalability. The devices show great response to pH changes with a wide dynamic range and high sensitivity. Biomarker detection is also demonstrated with clinically relevant sensitivity. Such results suggest that polysilicon nanoribbon devices exhibit great potential toward a highly efficient, reliable and sensitive biosensing platform.

scholarly journals Label-Free Assays on the BIND System

2004 ◽  
Vol 9 (6) ◽  
pp. 481-490 ◽  
Author(s):  
Brian T. Cunningham ◽  
Peter Li ◽  
Stephen Schulz ◽  
Bo Lin ◽  
Cheryl Baird ◽  
...  
Keyword(s):  
Fluorescent Dyes ◽  
Dynamic Range ◽  
Low Cost ◽  
High Sensitivity ◽  
Receptor Expression ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Small Molecule Screening ◽  
Guided Mode ◽  
Wide Range

Screening of biochemical interactions becomes simpler, less expensive, and more accurate when labels, such as fluorescent dyes, radioactive markers, and colorimetric reactions, are not required to quantify detected material. SRU Biosystems has developed a biosensor technology that is manufactured on continuous sheets of plastic film and incorporated into standard microplates and microarray slides to enable label-free assays to be performed with high throughput, high sensitivity, and low cost per assay. The biosensor incorporates a narrow band guided-mode resonance reflectance filter, in which the reflected color is modulated by the attachment/detachment of biochemical material to the surface. The technology offers 4 orders of linear dynamic range and uniformity within a plate, with a coefficient of variation of 2.5%. Using conventional biochemical immobilization surface chemistries, a wide range of assay applications are enabled. Small molecule screening, cell proliferation/cytotoxicity, enzyme activity screening, protein-protein interaction, and cell membrane receptor expression are among the applications demonstrated.

Sign in / Sign up

Export Citation Format

Share Document