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Machine Learning-Assisted array-based Detection of Proteins in Serum Using Functionalized MoS2 Nanosheets and Green Fluorescent Protein Conjugates

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ACS APPLIED NANO MATERIALS 2021年第4期4卷 3843-3851页

作者： Behera, Pradipta Singh, Krishna Kumar Pandit, Subhendu Saha, Diptarka Saini, Deepak Kumar De, Mrinmoy Indian Inst Sci Dept Organ Chem Bangalore 560012 Karnataka India Augusta Univ Vasc Biol Ctr Augusta GA 30912 USA Indian Inst Sci Mol Reprod Dev & Genet Bangalore 560012 Karnataka India Univ Illinois Dept Chem Urbana IL 61801 USA Univ Illinois Dept Stat Urbana IL 61801 USA

Abnormal concentrations of a specific protein or the presence of some biomarker proteins may indicate life-threatening diseases. Pattern-based detection of specific analytes using affinity-regulated receptors is one of the potential alternatives to specific antigen-antibody-based detection. In this report, we have schemed a sensor array by using various functionalized two-dimensional (2D)-MoS2 nanosheets and green fluorescent protein (GFP) as the receptor and the signal transducer, respectively. Two-dimensional MoS2 has been used as a promising candidate for recognition of the bioanalytes because of its high surface-to-volume ratio compared to those of other nanomaterials. Easy surface tunability of this material provides additional advantages to analyze the target of interest. The optimized 2D-MoS2-GFP conjugates are able to discriminate 15 different proteins at 50 nM concentration with a detection limit of 1 nM. Moreover, proteins in the binary mixture and in the presence of serum were discriminated successfully. Ten different proteins in serum media at relevant concentrations were classified successfully with 100% jackknifed classification accuracy, which proves the potentiality of the above system. We have also implemented and discussed the implication of using different machine learning models on the pattern recognition problem associated with array-based sensing.

关键词： two-dimensional MoS2 array-based sensing protein sensing pattern recognition machine learning

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A colorimetric supramolecular sensor array for anaesthetic drugs detection and classification

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SENSORS AND ACTUATORS B-CHEMICAL 2025年 440卷

作者： Gonzalez-Galindo, Carlos Duval, Emilie Bosco, Monica Swetha Ibrahim, Agop Auvray, Marie Naud-Martin, Delphine Mahuteau-Betzer, Florence Gagey-Eilstein, Nathalie Univ Paris Cite CNRS Unite Technol Chim & Biol St UTCBS InsermFac Pharm ParisU1267UMR 8258 F-75006 Paris France Univ PSL CNRS Inst Curie InsermU1196UMR9187 F-91400 Orsay France Univ Paris Saclay CNRS Inserm U1196UMR9187 F-91400 Orsay France LCMD ESPCI 10 Rue Vauquelin F-75005 Paris France Univ Paris Saclay CNRS Inst Alembert ENS Paris SaclayLuMIn F-91190 Gif Sur Yvette France Max Planck Inst Multidisciplinary Dept NanoBioPhoton Chromatin Labeling & Imaging Gottingen Germany

The global pharmaceutical industry has experienced significant growth, accompanied by a worrying increase in counterfeit medicines. Substandard medicines pose serious health risks, including poisoning, exacerbation of untreated conditions and mortality, particularly in regions with weak regulatory systems. Anaesthetics, essential to medical care, are particularly vulnerable to supply chain shortages and counterfeiting, highlighting the need for effective authentication strategies. Herein, we propose a colorimetric sensor-array based on a competitive displacement mechanism exploiting the supramolecular host-guest interactions between cucurbit[n]uril macrocycles and cationic multibranched chromogenic dyes. This approach exploits the competition between anaesthetic molecules and host-dye complexes to induce analyte-specific dye colorimetric changes. The resulting optical fingerprints, being a combination of all the signals of the host/dye complexes, processed by machine learning algorithms, allows for the detection, discrimination, and quantification of six anaesthetic molecules. This newly developed array thereby provides a potential tool for addressing issues related to drug counterfeiting and enhancing the reliability of pharmaceutical quality control.

关键词： array-based sensing Host-guest systems Cucurbit[ n ]urils Pattern recognition Counterfeiting Anaesthetics

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array-based sensing of Metastatic Cells and Tissues Using Nanoparticle-Fluorescent Protein Conjugates

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ACS NANO 2012年第9期6卷 8233-8240页

作者： Rana, Subinoy Singla, Arvind K. Bajaj, Avinash Elci, S. Gokhan Miranda, Oscar R. Mout, Rubui Yan, Bo Jirik, Frank R. Rotello, Vincent M. Univ Massachusetts Dept Chem Amherst MA 01003 USA Univ Calgary McCaig Inst Bone & Joint Hlth Dept Biochem & Mol Biol Calgary AB Canada

Rapid and sensitive methods of discriminating between healthy tissue and metastases are critical for predicting disease course and designing therapeutic strategies. We report here the use of an array of gold nanoparticle-green fluorescent protein elements to rapidly detect metastatic cancer cells (in minutes), as well as to discriminate between organ-specific metastases and their corresponding normal tissues through their overall intracellular proteome signatures. Metastases established in a new preclinical non-small-cell lung cancer metastasis model in athymic mice were used to provide a challenging and realistic testbed for clinical cancer diagnosis. Full differentiation between the analyte cell/tissue was achieved with as little as 200 ng of intracellular protein (similar to 1000 cells) for each nanoparticle, indicating high sensitivity of this sensor array. Notably, the sensor created a distinct fingerprint pattern for the normal and metastatic tumor tissues. Moreover, this array-based approach is unbiased, precluding the requirement of a priori knowledge of the disease biomarkers. Taken together, these studies demonstrate the utility of this sensor for creating fingerprints of cells and tissues in different states and present a generalizable platform for rapid screening amenable to microbiopsy samples.

关键词： array-based sensing metastasis tissue lysates gold nanoparticle

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Rapid Discrimination of Bacterial Drug Resistivity by array-based Cross-Validation Using 2D MoS2

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CHEMISTRY-A EUROPEAN JOURNAL 2022年第47期28卷 e202201386-e202201386页

作者： Behera, Pradipta Singh, Krishna Kumar Saini, Deepak Kumar De, Mrinmoy Indian Inst Sci Dept Organ Chem Bangalore 560012 Karnataka India Indian Inst Sci Mol Reprod Dev & Genet Bangalore 560012 Karnataka India Johns Hopkins Univ Sch Med Dept Cardiol Baltimore MD 21205 USA

The precise discrimination of microbes based on family, class and drug resistivity is essential for the early diagnosis of infectious diseases. Information about the type and strength of drug resistivity can help the analyst to prescribe a suitable antibiotic at the proper dosage to completely eradicate microbes without giving them a chance to gain further resistance. Herein, we propose a sensor array based on the use of cationic two-dimensional MoS2 units and green fluorescence protein as building blocks. Cationic surfaces of receptors with various functionality were suitable for tunable interaction with anionic surfaces of microbes. The array successfully discriminates six different bacterial strains. The versatile ability of the receptors to bind with the wild-type as well as the corresponding ampicillin-resistant strain contributed significantly to rapid detection with high sensitivity. The optimized array was able to classify five different types and three different extents of drug-resistant variants of Escherichia coli by using bacteria cells and lysates. Finally, we have introduced the cross identification method using both bacteria cells and lysates and we found a great enhancement of detection in sensitivity and accuracy. This is the first report of this approach, which can be extended to many other methods for better accuracy in array-based detection.

关键词： Keywords array-based sensing bacteria sensing drug-resistant bacteria 2D MoS2

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Functionalized Fluorescent Nanodots for Discrimination of Nitroaromatic Compounds

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ACS APPLIED NANO MATERIALS 2020年第3期3卷 2846-2856页

作者： Behera, Pradipta Mohanty, Ashutosh De, Mrinmoy Indian Inst Sci Dept Organ Chem Bangalore 560012 Karnataka India

Multiplexing the sensor array can save the time and sensor elements in detection of various unknowns. However, sometimes, that method compromises the sensitivity of a sensor system. Alternatively, a sequential on-off strategy can be applied in a sensor array to enhance the sensitivity. In this strategy, instead of separating individual sensor elements, sequential addition of quenching and masking agents to the pre-established sensor array can enhance the signal output information, sensitivity, and classification accuracy. Herein, three different quantum dots, that is, gold nanoclusters (AuNCs), MoS2 quantum dots (MQD) and WS2 quantum dots (WQD) were used as fluorescent receptors for the sensing of nitroaromatic compounds. These electron-rich quantum dots with versatile surface property provide an array based on the quenching efficiency of nitroaromatic compounds. By using standard array-based sensing, we were not able to classify a large number of nitroaromatic compounds, whereas 100% classification was achieved by employing the suitable surface functionality and sequential on-off strategy. Furthermore, we have studied the mechanism of sequential sensing. According to the optical study, the primary inner-filter effect plays an important role in the quenching of fluorescence intensity of quantum dots. Fluorescence lifetime measurement suggests that AuNCs exhibit the dynamic mode of quenching and transition-metal dichalcogenide quantum dots (MQD and WQD) exhibit the static mode of quenching. This developed methodology can be extended to sensing of other analytes.

关键词： array-based sensing quantum dots fluorescence turn on-off nitroaromatic compounds linear discriminant analysis (LDA)

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Differentiation of Cancer Stem Cells through Nanoparticle Surface Engineering

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ACS NANO 2020年第11期14卷 15276-15285页

作者： Geng, Yingying Amante, John J. Goel, Hira L. Zhang, Xianzhi Walker, Melanie R. Luther, David C. Mercurio, Arthur M. Rotello, Vincent M. Univ Massachusetts Mol & Cellular Biol Program Amherst MA 01003 USA Univ Massachusetts Dept Chem Amherst MA 01003 USA Univ Massachusetts Med Sch Dept Mol Cell & Canc Biol Worcester MA 01605 USA

Cancer stem cells (CSCs) are a crucial therapeutic target because of their role in resistance to chemo- and radiation therapy, metastasis, and tumor recurrence. Differentiation therapy presents a potential strategy for "defanging" CSCs. To date, only a limited number of small-molecule and nanomaterial-based differentiating agents have been identified. We report here the integrated use of nanoparticle engineering and hypothesis-free sensing to identify nanoparticles capable of efficient differentiation of CSCs into non-CSC phenotypes. Using this strategy, we identified a nanoparticle that induces CSC differentiation by increasing intracellular reactive oxygen species levels. Importantly, this unreported phenotype is more susceptible to drug treatment than either CSCs or non-CSCs, demonstrating a potentially powerful strategy for anticancer therapeutics.

关键词： array-based sensing phenotype nanoparticle surface engineering breast cancer cancer stem cell differentiation therapy

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Multichannel DNA Sensor array Fingerprints Cell States and Identifies Pharmacological Effectors of Catabolic Processes

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ACS SENSORS 2019年第12期4卷 3124-3132页

作者： Das Saha, Nilanjana Sasmal, Ranjan Meethal, Shafeekh Kulathinte Vats, Somya Gopinathan, Preethi V. Jash, Oishika Manjithaya, Ravi Gagey-Eilstein, Nathalie Agasti, Sarit S. Jawaharlal Nehru Ctr Adv Sci Res New Chem Unit Bangalore 560064 Karnataka India Jawaharlal Nehru Ctr Adv Sci Res Chem & Phys Mat Unit Bangalore 560064 Karnataka India Jawaharlal Nehru Ctr Adv Sci Res Mol Biol & Genet Unit Bangalore 560064 Karnataka India Jawaharlal Nehru Ctr Adv Sci Res Sch Adv Mat SAMat Bangalore 560064 Karnataka India Univ Paris 05 UMR S 1139 Fac Sci Pharmaceut & Biol Sorbonne Paris CiteINSERM3PHM 4 Ave Observ F-75006 Paris France Pocker Sahib Mem Orphanage PSMO Coll Post Grad & Res Dept Chem Malappuram 676306 Kerala India

Cells at disease onset are often associated with subtle changes in the expression level of a single or few molecular components, making traditionally used biomarker-driven clinical diagnosis a challenging task. We demonstrate here the design of a DNA nanosensor array with multichannel output that identifies the normal or pathological state of a cell based on the alteration of its global proteomic signature. Fluorophore-encoded single-stranded DNA (ssDNA) strands were coupled via supramolecular interaction with a surface-functionalized gold nanoparticle quencher to generate this integrated sensor array. In this design, ssDNA sequences exhibit dual roles, where they provide differential affinities with the receptor gold nanoparticle as well as act as transducer elements. The unique interaction mode of the analyte molecules disrupts the noncovalent supramolecular complexation, generating simultaneous multichannel fluorescence output to enable signature-based analyte identification via a linear discriminant analysis-based machine learning algorithm. Different cell types, particularly normal and cancerous cells, were effectively distinguished using their fluorescent fingerprints. Additionally, this DNA sensor array displayed excellent sensitivity to identify cellular alterations associated with chemical modulation of catabolic processes. Importantly, pharmacological effectors, which could modulate autophagic flux, have been effectively distinguished by generating responses from their global protein signatures. Taken together, these studies demonstrate that our multichannel DNA nanosensor is well suited for rapid identification of subtle changes in a complex mixture and thus can be readily expanded for point-of-care clinical diagnosis, high-throughput drug screening, or predicting the therapeutic outcome from a limited sample volume.

关键词： DNA nanosensor array-based sensing fluorescence fingerprint cell discrimination autophagic flux machine learning

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Nano-Graphene Oxide based Multichannel Sensor arrays towards sensing of Protein Mixtures

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CHEMISTRY-AN ASIAN JOURNAL 2019年第4期14卷 553-560页

作者： Behera, Pradipta De, Mrinmoy Indian Inst Sci Dept Organ Chem Bangalore 560012 Karnataka India

Optical array-based sensors are attractive candidates for the detection of various bio-analytes due to their convenient fabrication and measurements. For array-based sensors, multichannel arrays are more advantageous and used frequently in many electronic sensors. But most reported optically array based sensors are constructed on a single channel array. This difficulty is mainly instigated from the overlap in optical responses. In this report we have used nano-graphene oxide (nGO) and suitable fluorophores as sensor elements to construct a multichannel sensor array for the detection of protein analytes. By using the optimized multichannel array we are able to detect different proteins and mixtures of proteins with 100 % classification accuracy at sub-nanomolar concentration. This modified method expedites the sensing analysis as well as minimizes the use of both analyte and sensor elements in array-based protein sensing. We have also used this system for the single channel array-based sensing to compare the sensitivity and the efficacy of these two systems for other applications. This work demonstrated an intrinsic trade-off associated with these two methods which may be necessary to balance for array-based analyte detections.

关键词： array-based sensing FRET efficiency linear discriminant analysis (LDA) nano-graphene oxide protein sensing

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In Situ Synthesis of Amino Acid Functionalized Carbon Dots with Tunable Properties and Their Biological Applications

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ACS APPLIED BIO MATERIALS 2019年第8期2卷 3393-3403页

作者： Pandit, Subrata Behera, Pradipta Sahoo, Jagabandhu De, Mrinmoy Indian Inst Sci Dept Organ Chem Bangalore 560012 Karnataka India

Emissive carbon dots (C-Dots) are known for displaying versatile properties, which have been widely utilized in many applications such as bioimaging, light-emitting devices, and photocatalysis. Further functionalization can tune their physical and chemical properties, which play the key role in many biologically and chemically relevant applications. Amino acids provide an attractive means for introducing functionality with a structural diversity. In this work, water-soluble emissive C-Dots were synthesized from pyrolysis of citric acid in the presence of various amino acids under hydrothermal conditions. We established that the diverse functionality-bearing polyamides and the polyester backbone of C-Dots are the origin of optical properties with a high quantum yield. The amino acid based C-Dots were systematically characterized using various analytical methods to confirm the core structure as well as the functionality. The results show that, depending on functionalization, the quantum yield can be varied and enhanced up to 62% and surface charge and hydrophobicity can be tuned. Most importantly, we observed a correlation between the quantum yield and properties of the side chain residue of amino acids such as hydrophobicity index and volume. Furthermore, it was found that the synthesized, diversely functionalized C-Dots exhibit no cellular toxicity and can be used for cell imaging. Due to variable surface functionality, we have also applied these C-Dots for array-based protein sensing. Overall, based on this reported method, we can easily tune the optical as well as surface properties of C-Dots, which will be suitable for many future applications.

关键词： carbon dot surface functionalization structure-property correlation bioimaging array-based sensing

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Two 3d-4f metal-organic frameworks as fluorescent sensor array for the discrimination of phosphates based on different response patterns

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SENSORS AND ACTUATORS B-CHEMICAL 2020年 324卷 128757-128757页

作者： Du, Shi Zhe Sun, Zhe Han, Lei Qing, Min Luo, Hong Qun Li, Nian Bing Southwest Univ Sch Chem & Chem Engn Key Lab Ecoenvironm Three Gorges Reservoir Reg Minist Educ Chongqing 400715 Peoples R China

Both organic and inorganic phosphates play important roles in biological activities. Considering the conventional methods are not very useful for identifying them from their analogues, the sensor array strategy has emerged in recent years, which is able to distinguish chemical species with similar structure or chemical properties. We propose a fluorescence sensor array based on two 3d-4f metal-organic frameworks (MOFs) by recording their direct one-step fluorescence changes with the addition of various phosphates. With the introduction of d-metal ions in the sensor unit synthesis process, two 3d-4f MOFs display higher sensitivity and noticeable fluorescence differences to five phosphates than the homometallic MOFs. Phosphates show diverse affinities to sensor units, forming the basis of differential sensing. The signals are much easier to collect, enabling the sensor array to simply accomplish the identification. Through statistical analysis, the sensor array is proved to be excellent in discriminating individual phosphate and mixture. Discrimination of five phosphates is successfully performed in serum samples to illustrate the practicability of the sensor array. This work presents an efficient and reliable approach for simultaneous detection of different phosphates, which can be extended to devise other array-based sensing methods.

关键词： Phosphates Fluorescent sensor array Differential sensing 3d-4f metal-organic frameworks array-based sensing

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