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"Bhat, Ramray"
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Tunable encapsulation of sessile droplets with solid and liquid shells
2023
Droplet encapsulations using liquid or solid shells are of significant interest in microreactors, drug delivery, crystallization, and cell growth applications. Despite progress in droplet-related technologies, tuning micron-scale shell thickness over a large range of droplet sizes is still a major challenge. In this work, we report capillary force assisted cloaking using hydrophobic colloidal particles and liquid-infused surfaces. The technique produces uniform solid and liquid shell encapsulations over a broad range (5–200 μm shell thickness for droplet volume spanning over four orders of magnitude). Tunable liquid encapsulation is shown to reduce the evaporation rate of droplets by up to 200 times with a wide tunability in lifetime (1.5 h to 12 days). Further, we propose using the technique for single crystals and cell/spheroid culture platforms. Stimuli-responsive solid shells show hermetic encapsulation with tunable strength and dissolution time. Moreover, scalability, and versatility of the technique is demonstrated for on-chip applications.
Encapsulated liquids are important for several microreactor applications, including (bio)chemistry in confined spaces. Here, the authors report on oil-infused particle shells that allow control of shell thickness, stability, and permeability for applications in crystal growth and cell cultivation.
Journal Article
Circulating Tumor Cell cluster phenotype allows monitoring response to treatment and predicts survival
2019
Circulating tumor cells (CTCs) are putative markers of tumor prognosis and may serve to evaluate patient’s response to chemotherapy. CTCs are often detected as single cells but infrequently as clusters and are indicative of worse prognosis. In this study, we developed a short-term culture of nucleated blood cells which was applied to blood samples from breast, lung, esophageal and bladder cancer patients. Clusters of different degrees of compactness, classified as very tight, tight and loose were observed across various cancer types. These clusters show variable expression of cytokeratins. Cluster formation from blood samples obtained during the course of chemotherapy was found to be associated with disease progression and shorter overall survival. The short-term cultures offer a robust and highly reliable method for early prediction of treatment response in different cancer types.
Journal Article
An interplay of resource availability, population size and mutation rate potentiates the evolution of metabolic signaling
by
Kumawat, Bhaskar
,
Bhat, Ramray
in
Analysis
,
Animal Systematics/Taxonomy/Biogeography
,
Artificial life
2021
Background
Asexually reproducing populations of single cells evolve through mutation, natural selection, and genetic drift. Environmental conditions in which the evolution takes place define the emergent fitness landscapes. In this work, we used Avida—a digital evolution framework—to uncover a hitherto unexplored interaction between mutation rates, population size, and the relative abundance of metabolizable resources, and its effect on evolutionary outcomes in small populations of digital organisms.
Results
Over each simulation, the population evolved to one of several states, each associated with a single dominant phenotype with its associated fitness and genotype. For a low mutation rate, acquisition of fitness by organisms was accompanied with, and dependent on, an increase in rate of genomic replication. At an increased mutation rate, phenotypes with high fitness values were similarly achieved through enhanced genome replication rates. In addition, we also observed the frequent emergence of suboptimal fitness phenotype, wherein neighboring organisms signaled to each other information relevant to performing metabolic tasks. This metabolic signaling was vital to fitness acquisition and was correlated with greater genotypic and phenotypic heterogeneity in the population. The frequency of appearance of signaling populations increased with population size and with resource abundance.
Conclusions
Our results reveal a minimal set of environment–genotype interactions that lead to the emergence of metabolic signaling within evolving populations.
Journal Article
Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins
2020
Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of N-linked glycosylations or N-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. We then investigated the basis of mutual exclusivity between disorder and N-glycosites on the basis of amino acid distribution: when compared with control ordered residue stretches without any N-glycosites, residue neighborhoods surrounding N-glycosites showed a depletion of bulky, hydrophobic and disorder-promoting amino acids and an enrichment for flexible and accessible residues that are frequently found in coiled structures. When compared with control disordered residue stretches without any N-glycosites, N-glycosite neighborhoods were depleted of charged, polar, hydrophobic and flexible residues and enriched for aromatic, accessible and order-promoting residues with a tendency to be part of coiled and β structures. N-glycosite neighborhoods also showed greater phylogenetic conservation among amniotes, compared with control ordered regions, which in turn were more conserved than disordered control regions. Our results lead us to propose that unique primary structural compositions and differential propensities for evolvability allowed for the mutual spatial exclusion of N-glycosite neighborhoods and disordered stretches.
Journal Article
Extracellular matrix mediates moruloid-blastuloid morphodynamics in malignant ovarian spheroids
by
Narayanan, Shruthi
,
Vadaparty, Annapurna
,
Langthasa, Jimpi
in
Ascites
,
Basement membranes
,
Blastula - metabolism
2021
Ovarian cancer metastasizes into peritoneum through dissemination of transformed epithelia as multicellular spheroids. Harvested from the malignant ascites of patients, spheroids exhibit startling features of organization typical to homeostatic glandular tissues: lumen surrounded by smoothly contoured and adhered epithelia. Herein, we demonstrate that cells of specific ovarian cancer lines in suspension, aggregate into dysmorphic solid “moruloid” clusters that permit intercellular movement, cell penetration, and interspheroidal coalescence. Moruloid clusters subsequently mature into “blastuloid” spheroids with smooth contours, a temporally dynamic lumen and immotile cells. Blastuloid spheroids neither coalesce nor allow cell penetration. Ultrastructural examination reveals a basement membrane-like extracellular matrix coat on the surface of blastuloid, but not moruloid, spheroids. Quantitative proteomics reveals down-regulation in ECM protein Fibronectin-1 associated with the moruloid-blastuloid transition; immunocytochemistry also confirms the relocalization of basement membrane ECM proteins: collagen IV and laminin to the surface of blastuloid spheroids. Fibronectin depletion accelerates, and enzymatic basement membrane debridement impairs, lumen formation, respectively. The regulation by ECM dynamics of the morphogenesis of cancer spheroids potentially influences the progression of the disease.
Journal Article
Author Correction: Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins
by
Ghosh, Sujasha
,
Akhter, Yusuf
,
Bhat, Ramray
in
Author
,
Author Correction
,
Humanities and Social Sciences
2020
An amendment to this paper has been published and can be accessed via a link at the top of the paper.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Journal Article
Rheological transition driven by matrix makes cancer spheroids resilient under confinement
by
Langthasa, Jimpi
,
Vidhipriya, Kottpalli
,
Bhat, Ramray
in
Atomic force microscopy
,
Cadherins - metabolism
,
Cell Adhesion
2025
Cancer metastasis through confining peritoneal microenvironments is mediated by spheroids: clusters of disseminated cells. Ovarian cancer spheroids are frequently cavitated; such blastuloid morphologies possess an outer ECM coat. We investigated the effects of these spheroidal morphological traits on their mechanical integrity. Atomic force microscopy showed blastuloids were elastic compared with their prefiguring lumenless moruloid counterparts. Moruloids flowed through microfluidic setups mimicking peritoneal confinement, exhibited asymmetric cell flows during entry, were frequently disintegrated, and showed an incomplete and slow shape recovery upon exit. In contrast, blastuloids exhibited size-uncorrelated transit kinetics, rapid and efficient shape recovery upon exit, symmetric cell flows, and lesser disintegration. Blastuloid ECM debridement phenocopied moruloid traits including lumen loss and greater disintegration. Multiscale computer simulations predicted that higher intercellular adhesion and dynamical lumen make blastuloids resilient. Blastuloids showed higher E-cadherin expression, and their ECM removal decreased membrane E-cadherin localization. E-cadherin knockdown also decreased lumen formation and increased spheroid disintegration. Thus, the spheroidal ECM drives its transition from a labile viscoplastic to a resilient elastic phenotype, facilitating their survival within spatially constrained peritoneal flows.
Journal Article