About

Ashok Samuel is a Research Associate Professor in the Department of Bioengineering at the University of Illinois Urbana-Champaign. His primary research area is biomedical imaging, specifically biophotonics, with a focus on cancer, live-cell imaging, molecular imaging, and tumor microenvironments. His work integrates optical imaging techniques to develop interdisciplinary solutions for detecting and treating health issues. Samuel has a background in Raman Spectroscopy, Polymer Chemistry, and Physical Chemistry from the Indian Institute of Science, Bangalore, where he earned his Ph.D. between 2006 and 2012. Since 2023, he has been serving as a Research Associate Professor at UIUC, after previously working as an Assistant Professor (Research) at Waseda University in Tokyo, Japan. His research involves advanced Raman imaging to identify biochemically unique cell phenotypes, studying phenotype-dependent drug responses in cancer, and capturing cell morphology dynamics using high temporal resolution imaging. Samuel's contributions include developing techniques for direct intracellular detection of biomolecules and liquid-liquid phase separated membraneless organelles, as well as investigating mechanisms of calcium phosphate calcification in human tissues. His work aims to provide innovative solutions in biomedical imaging and cancer research.

Research topics

• Chemistry
• Materials science
• Biology
• Chemical engineering
• Biophysics

Selected publications

• Single-shot Quantitative Gradient Phase Microscopy (QGPM) to Monitor Cellular Kinetics

  Microscopy and Microanalysis · 2024-07-01

  article
  PublisherDOI

• Capturing cell morphology dynamics with high temporal resolution using single-shot quantitative phase gradient imaging

  Journal of Biomedical Optics · 2024-07-16 · 6 citations

  articleOpen access

  SignificanceLabel-free quantitative phase imaging can potentially measure cellular dynamics with minimal perturbation, motivating efforts to develop faster and more sensitive instrumentation. We characterize fast, single-shot quantitative phase gradient microscopy (ss-QPGM) that simultaneously acquires multiple polarization components required to reconstruct phase images. We integrate a computationally efficient least squares algorithm to provide real-time, video-rate imaging (up to 75 frames/s). The developed instrument was used to observe changes in cellular morphology and correlate these to molecular measures commonly obtained by staining.AimWe aim to characterize a fast approach to ss-QPGM and record morphological changes in single-cell phase images. We also correlate these with biochemical changes indicating cell death using concurrently acquired fluorescence images.ApproachHere, we examine nutrient deprivation and anticancer drug-induced cell death in two different breast cell lines, viz., M2 and MCF7. Our approach involves in-line measurements of ss-QPGM and fluorescence imaging of the cells biochemically labeled for viability.ResultsWe validate the accuracy of the phase measurement using a USAF1951 pattern phase target. The ss-QPGM system resolves 912.3 lp/mm, and our analysis scheme accurately retrieves the phase with a high correlation coefficient (∼0.99), as measured by calibrated sample thicknesses. Analyzing the contrast in phase, we estimate the spatial resolution achievable to be 0.55 μm for this microscope. ss-QPGM time-lapse live-cell imaging reveals multiple intracellular and morphological changes during biochemically induced cell death. Inferences from co-registered images of quantitative phase and fluorescence suggest the possibility of necrosis, which agrees with previous findings.ConclusionsLabel-free ss-QPGM with high-temporal resolution and high spatial fidelity is demonstrated. Its application for monitoring dynamic changes in live cells offers promising prospects.

  PublisherOA PDFDOI

• Editorial: Exploring complex biosphere molecular signaling networks: plant-microbes symbiosis at microscopic to macroscopic levels

  Frontiers in Plant Science · 2023-05-26 · 3 citations

  editorialOpen accessSenior authorCorresponding

  Plants have evolved to live on earth using basic chemicals, such as, CO2, water, and minerals in air and soil. This knowledge helped human beings develop industrial agriculture to build and maintain civilizations, to domesticate animals, and to meet the food demands of growing population. However, crop production engineering using chemical fertilizers/pesticides, overexploitation of soil resources disregarding subtle balances in the ecosystem, and climate change have created a crisis (Timmis and Ramos, 2021). Our realization that soil is a highly interconnected ecosystem with interspecies chemical exchange through, for instance, symbiosis, has opened avenues for developing sustainable agricultural practices protecting the environment (Zipfel and Oldroyd, 2017). Moreover, the quality of the agricultural produces depends heavily on the biotic and abiotic environmental factors plants experience in the environment. The environmental factors that affect crops need to be assessed scientifically and documented, rather than relying on sensory perception to assess nutritional quality of the produces. Further, fundamental investigations should also be conducted to better understand the symbiosis between microbes and plants from a molecular perspective. Studies in the recent past have revealed several molecular aspects of soil microbe entry into legume plants' root system, subsequent nodulation of root, and effective nitrogen fixation. Discovery of nod factor (e.g., oligosaccharide derivative produced by S. meliloti) revealed the molecular mechanism of microbe entrapment in root hairs.Subsequent studies revealed the role of symbiosis entry receptors (e.g., LYK3), hence the corresponding genes, in the effective infection process. Similarly, phosphate levels in the environment and Ca 2+ spiking are essential for the causing appropriate changes in the root hair phenotype and for infection to proceed beyond the microbe entrapment in root hairs (Gilroy and Jones, 2000;Parry, 2018;Bono et al., 2020;de Bruijn, 2020bde Bruijn, , 2020a. Next generation smart analytical tools are also being developed for automated diagnosis of plants by measuring specific molecular species (e.g., volatile organic compounds (VOC), plant metabolites, etc.) (Lew et al., 2020). Accessible and affordable robots, controlled by scientific data-driven artificial intelligence modules, are being developed for specific applications in agriculture.Various plant developmental stages -seed germination to fruit ripening -produce distinct chemicals (e.g., ethylene). At several instances, chemical profile changes can be correlated with pathogen infection much before real symptoms starts to appear. For instance, tomato leaves infected with three different pathogens showed accurately identifiable VOC profiles before visible symptoms appeared (Li et al., 2019). Handheld and smartphone-based spectrometers along with spectral matching applications through mathematical routines find unique applications in agricultural fields (Samuel et al., 2021) abiotic stresses, such as, nitrogen deficiency (ND) and drought, and biotic stresses, such as, aphid infestation and viral infections, affects common wheat. Changes in lutein, chlorophyll, pheophytin, and beta-carotene were estimated with high-pressure liquid chromatography (HPLC). Aphid infestation was found to be the most detrimental among the stresses investigated. Raman spectral data collected directly from wheat leaves with a handheld spectrometer indicated similar reduction in carotenoid band intensity suggesting possible field applications of the technique.Equally important is estimating chemical composition of nutritionally and medically important molecules in plant produces. If spectral signatures corresponding to a molecule of interest is known, then a spectrometer can be calibrated (e.g., with HPLC, for instance) and predictive models (e.g., partial least square methods, machine learning modules) can be built, which will then allow subsequent quantitative chemical analysis of crops directly from spectral intensities. Ming, et al. Correlating genetic information and metabolic information is an important area requiring exploratory future studies.The research articles published in this Research Topic provides specific examples of utility and adaptability of general analytical techniques in agricultural research and field applications. Further, a literature review by Chen, et al. discusses the effective utilization of agricultural residues, such as, straw return and straw biochar, for improving soil properties. Automated field deployment of sensitive analytical laboratory techniques by integrating robotics and artificial intelligence is expected to revolutionize sustainable agricultural initiatives.

  PublisherOA PDFDOI

• Mycelial differentiation linked avermectin production in <i>Streptomyces avermitilis</i> studied with Raman imaging

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-09-30

  preprintOpen access

  Abstract Streptomyces avermitilis is a gram-positive bacterium that undergoes complex physiological and morphological differentiation during its life cycle, which has implications in secondary metabolites production. Avermectin, produced by S. avermitilis , is widely used as an anthelmintic and insecticidal agent. In this study, we have applied Raman microspectroscopic imaging to elucidate the correlation between production of avermectin and the morphological differentiation in S. avermitilis . We demonstrate distinctive variations in the localization of avermectin at various morphological stages, such as, substrate mycelium, spore-bearing mycelium, spiral spore chains under solid culture conditions. Under liquid culture condition, however, avermectin is detected only in mycelia after early MII stage of differentiation. Morphological differentiation was observed in liquid and solid cultures, but the chemical profiles of the mycelia were substantially different. Spherical bodies containing avermectin with characteristically different chemical composition to that of spores were also observed under solid culture, which suggests possible release of extracellular vesicles (EVs). Key points Avermectin production is regulated during mycelial differentiation Liquid and solid culture conditions affects mycelial differentiation Raman microspectroscopic analysis reveals localization profiles of avermectin

  PublisherOA PDFDOI

• Mycelial differentiation linked avermectin production in Streptomyces avermitilis studied with Raman imaging

  Applied Microbiology and Biotechnology · 2022-12-07 · 8 citations

  article
  PublisherDOI

• Raman Microspectroscopy Imaging Analysis of Extracellular Vesicles Biogenesis by Filamentous Fungus <i>Penicilium chrysogenum</i>

  Advanced Biology · 2022-03-11 · 15 citations

  articleOpen access1st author

  The mechanism of production of extracellular vesicles (EVs) and their molecular contents are of great interest due to their diverse roles in biological systems and are far from being completely understood. Even though cellular cargo releases mediated by EVs have been demonstrated in several cases, their role in secondary metabolite production and release remains elusive. In this study, this aspect is investigated in detail using Raman microspectroscopic imaging. Considerable evidence is provided to suggest that the release of antibiotic penicillin by the filamentous fungus Penicillium chrysogenum involves EVs. Further, the study also reveals morphological modifications of the fungal body during biogenesis, changes in cell composition at the locus of biogenesis, and major molecular contents of the released EVs. The results suggest a possible general role of EVs in the release of antibiotics from the producing organisms.

  PublisherOA PDFDOI

• Direct intracellular detection of biomolecule specific bound-water with Raman spectroscopy

  Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · 2022-09-12 · 6 citations

  article1st authorCorresponding
  PublisherDOI

• Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis

  Scientific Reports · 2022-11-14 · 24 citations

  articleOpen access

  Spatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical applications. However, despite the advantages of long-term storage at room temperature, FFPE tissues may be severely damaged by methylene crosslinking and provide less gene information than fresh-frozen tissues. In this study, we proposed a sensitive FFPE micro-tissue RNA-seq method that combines the punching of tissue sections (diameter: 100 μm) and the direct construction of RNA-seq libraries. We evaluated a method using mouse liver tissues at two years after fixation and embedding and detected approximately 7000 genes in micro-punched tissue-spots (thickness: 10 μm), similar to that detected with purified total RNA (2.5 ng) equivalent to the several dozen cells in the spot. We applied this method to clinical FFPE specimens of lung cancer that had been fixed and embedded 6 years prior, and found that it was possible to determine characteristic gene expression in the microenvironment containing tumor and non-tumor cells of different morphologies. This result indicates that spatial gene expression analysis of the tumor microenvironment is feasible using FFPE tissue sections stored for extensive periods in medical facilities.

  PublisherOA PDFDOI

• Raman Microspectroscopy Imaging Analysis of Extracellular Vesicles Biogenesis by Filamentous Fungus <i>Penicilium chrysogenum</i> (Adv. Biology 6/2022)

  Advanced Biology · 2022-06-01

  articleOpen access1st authorCorresponding

  Extracellular Vesicles Biogenesis In article 2101322, Takeyama and co-workers study living cells that communicate with their surroundings by sending chemical messages. They show extracellular vesicles mediated antibiotic penicillin release from Penicillium chrysogenum fungus and demonstrate the exquisite potential of Raman micro-spectroscopy. Simultaneous detection of multiple molecules with this technique holds great promise in the chemical profiling of living systems.

  PublisherOA PDFDOI

• Direct imaging of intracellular RNA, DNA, and liquid–liquid phase separated membraneless organelles with Raman microspectroscopy

  Communications Biology · 2022-12-17 · 27 citations

  articleOpen access1st authorCorresponding

  Methodologies for direct intracellular imaging of RNA and DNA are necessary for the advancement of bioimaging. Here we show direct label-free imaging of RNA and DNA in single cells by isolating their accurate Raman spectra. Raman images of DNA from interphase cells show intact nucleus, while those from mitotic cells reveal condensed chromosome. The condensed chromosome images are accurate enough to assign the stage of mitotic cell division (e.g., metaphase). Raman spectral features indicate B-DNA double helical conformational form in all the cell lines investigated here. The Raman images of RNAs, on the other hand, reveal liquid-liquid phase separated (LLPS) membraneless organelles in interphase cells, which disappears during mitosis. Further, the Raman spectrum of proteins from the intracellular LLPS organelles indicates slight enrichment of amyloid-like secondary structural features. Vibrational imaging of intracellular DNA and RNA simultaneously would open myriad of opportunities for examining functional biochemical aspects of cells and organelles.

  PublisherOA PDFDOI

Frequent coauthors

• Haruko Takeyama

  Waseda University

  24 shared

• Masahiro Ando

  Waseda University

  19 shared

• Shumpei Horii

  Waseda University

  10 shared

• Yōko Takahashi

  8 shared

• A Take

  Kitasato University

  8 shared

• Atsuko Matsumoto

  Kitasato Institute Hospital

  8 shared

• Takuji Nakashima

  Kitasato Institute Hospital

  6 shared

• S. Ramakrishnan

  Indian Institute of Science Bangalore

  5 shared

Education

• phd, inorganic and physical chemistry

  Indian Institute of Science

  2012

Awards & honors

• Early Career Researcher Award, Society for Applied Spectrosc…