Manu Prakash

All Publications

• Ice gliding diatoms establish record-low temperature limits for motility in a eukaryotic cell. Proceedings of the National Academy of Sciences of the United States of America Zhang, Q., Leng, H. T., Li, H., Arrigo, K. R., Prakash, M. 2025; 122 (37): e2423725122

  Abstract

  Despite periods of permanent darkness and extensive ice coverage in polar environments, photosynthetic ice diatoms display a remarkable capability of living inside the ice matrix. How these organisms navigate such hostile conditions with limited light and extreme cold remains unknown. Using a custom subzero temperature microscope during an Arctic expedition, we present the finding of motility at record-low temperatures in a Eukaryotic cell. By characterizing the gliding motility of several ice diatom species, collected from ice cores in the Chukchi Sea, we record that they retain motility at temperatures as low as [Formula: see text]15 °C. Remarkably, ice diatoms can glide on ice substrates, a capability absent in temperate diatoms of the same genus. This unique ability arises from adaptations in extracellular mucilage that allow ice diatoms to adhere to ice, essential for gliding. Even on glass substrates where both cell types retain motility at freezing temperatures, ice diatoms move an order of magnitude faster, with their optimal motility shifting toward colder temperatures. Combining field and laboratory experiments with thermo-hydrodynamic modeling, we reveal adaptive strategies that enable gliding motility in cold environments. These strategies involve increasing internal energy efficiency with minimal changes in heat capacity and activation enthalpy, and reducing external dissipation by minimizing the temperature sensitivity of mucilage viscosity. The finding of diatoms' ice gliding motility opens new routes for understanding their survival within a harsh ecological niche and their migratory responses to environmental changes. Our work highlights the robust adaptability of ice diatoms in one of Earth's most extreme settings.

  View details for DOI 10.1073/pnas.2423725122

  View details for PubMedID 40924446

• Cellular Olympics: Ultrafast Cellular Motility Across the Tree of Life. Annual review of microbiology Chang, R., Prakash, M. 2025

  Abstract

  Surprisingly, many single-celled organisms and specialized cell types can achieve speed and acceleration significantly faster than those of multicellular animals. These remarkable cellular machines must integrate energy storage and amplification in actuation, latches for triggered release, and energy dissipation without failure-all implemented in macromolecular assemblies inside a single cell. In this review, we first map the atlas of single cells across the tree of life that use ultrafast motility. We then quantitatively compare extreme acceleration, speed, area strain rate, volume expansion strain rate, and density change rate among single cells. Next, we generalize these ideas by placing various trigger, actuation, and dissipation mechanisms within a unified framework. We conclude with a detailed summary of the diverse functions enabled by ultrafast cellular motility, providing a comprehensive foundation for understanding extreme biophysics and its diverse role at the cellular scale.

  View details for DOI 10.1146/annurev-micro-041020-021038

  View details for PubMedID 40825357

• Microscopy with microfluidics in microgravity using FlightScope. NPJ microgravity Wareing, T., Stokes, A., Crompton, K. E., Murphy, K., Dawson, J., Ugurluoglu, Y. F., Richardson, C., Li, H., Prakash, M., Wollman, A. J. 2025; 11 (1): 13

  Abstract

  With planned missions to the moon and Mars, it has never been more important to study the impact of microgravity on biological organisms. Parabolic flights are one of the most accessible microgravity research platforms but present challenges: short periods of microgravity and aircraft vibration. Live-imaging is necessary to readout any real-time phenotypes so we developed FlightScope, a new microscopy and microfluidics platform to study dynamic cellular processes in microgravity.

  View details for DOI 10.1038/s41526-025-00470-3

  View details for PubMedID 40328826

  View details for PubMedCentralID PMC12056092

• Interview with Manu Prakash JOURNAL OF CELL SCIENCE Prakash, M. 2025; 138 (6)

  View details for DOI 10.1242/jcs.263898

  View details for Web of Science ID 001463302600011

• A genetic and microscopy toolkit for manipulating and monitoring regeneration in Macrostomum lignano. Cell reports Hall, R. N., Li, H., Chai, C., Vermeulen, S., Bigasin, R. R., Song, E. S., Sarkar, S. R., Gibson, J., Prakash, M., Fire, A. Z., Wang, B. 2024; 43 (11): 114892

  Abstract

  Live imaging of regenerative processes can reveal how animals restore their bodies after injury through a cascade of dynamic cellular events. Here, we present a comprehensive toolkit for live imaging of tissue regeneration in the flatworm Macrostomum lignano, including a high-throughput cloning pipeline, targeted cellular ablation, and advanced microscopy solutions. Using tissue-specific reporter expression, we examine how various structures regenerate. Enabled by a custom luminescence/fluorescence microscope, we overcome intense stress-induced autofluorescence to demonstrate genetic cellular ablation and reveal the limited regenerative capacity of neurons and their essential role during wound healing, contrasting muscle cells' rapid regeneration after ablation. Finally, we build an open-source tracking microscope to continuously image freely moving animals throughout the week-long process of regeneration, quantifying kinetics of wound healing, nerve cord repair, body regeneration, growth, and behavioral recovery. Our findings suggest that nerve cord reconnection is highly robust and proceeds independently of regeneration.

  View details for DOI 10.1016/j.celrep.2024.114892

  View details for PubMedID 39427313

• ESPressoscope: A small and powerful approach for in situ microscopy. PloS one Li, E., Saggiomo, V., Ouyang, W., Prakash, M., Diederich, B. 2024; 19 (10): e0306654

  Abstract

  Microscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We address this challenge by investigating the feasibility of using a simple microcontroller board not only as a portable and field-ready digital microscope, but furthermore as a versatile platform which can easily be adapted to a variety of imaging applications. By adding a few external components, we demonstrate that a low-cost ESP32 camera board can be used to build an autonomous in situ platform for digital time-lapse imaging of cells. Our prototype of this approach, which we call ESPressoscope, can be adapted to applications ranging from monitoring incubator cell cultures in the lab to observing ecological phenomena in the sea, and it can be adapted for other techniques such as microfluidics or spectrophotometry. Our prototype of the ESPressoscope concept achieves a low power consumption and small size, which makes it ideal for field research in environments and applications where microscopy was previously infeasible. Its Wi-Fi connectivity enables integration with external image processing and storage systems, including on cloud platforms when internet access is available. Finally, we present several web browser-based tools to help users operate and manage our prototype's software. Our findings demonstrate the potential for low-cost, portable microscopy solutions to enable new and more accessible experiments for biological and analytical applications.

  View details for DOI 10.1371/journal.pone.0306654

  View details for PubMedID 39413076

• Inflation-induced motility for long-distance vertical migration. Current biology : CB Larson, A. G., Chajwa, R., Li, H., Prakash, M. 2024

  Abstract

  The vertical migrations of pelagic organisms play a crucial role in shaping marine ecosystems and influencing global biogeochemical cycles. They also form the foundation of what might be the largest daily biomass movement on Earth. Surprisingly, among this diverse group of organisms, some single-cell protists can transit depths exceeding 50m without employing flagella or cilia. How these non-motile cells perform large migrations remains unknown. It has been previously proposed that this capability might rely on the cell's ability to regulate its internal density relative to seawater. Here, using the dinoflagellate algae Pyrocystis noctiluca as a model system, we discover a rapid cell inflation event post cell division, during which a single plankton cell expands its volume 6-fold in less than 10min. We demonstrate this rapid cellular inflation is the primary mechanism of density control. This self-regulated cellular inflation selectively imports fluid less dense than surrounding seawater and can thus effectively sling-shot a cell and reverse sedimentation within minutes. To accommodate its dramatic cellular expansion, Pyrocystis noctiluca possesses a unique reticulated cytoplasmic architecture that enables a rapid increase in overall cell volume without diluting its cytoplasmic content. We further present a generalized mathematical framework that unifies cell-cycle-driven density regulation, stratified ecology, and associated cell behavior in the open ocean. Our study unveils an ingenious strategy employed by a non-motile plankton to evade the gravitational sedimentation trap, highlighting how precise control of cell size and cell density can enable long-distance migration in the open ocean.

  View details for DOI 10.1016/j.cub.2024.09.046

  View details for PubMedID 39423814

• Hidden comet tails of marine snow impede ocean-based carbon sequestration. Science (New York, N.Y.) Chajwa, R., Flaum, E., Bidle, K. D., Van Mooy, B., Prakash, M. 2024; 386 (6718): eadl5767

  Abstract

  Gravity-driven sinking of "marine snow" sequesters carbon in the ocean, constituting a key biological pump that regulates Earth's climate. A mechanistic understanding of this phenomenon is obscured by the biological richness of these aggregates and a lack of direct observation of their sedimentation physics. Utilizing a scale-free vertical tracking microscopy in a field setting, we present microhydrodynamic measurements of freshly collected marine snow aggregates from sediment traps. Our observations reveal hitherto-unknown comet-like morphology arising from fluid-structure interactions of transparent exopolymer halos around sinking aggregates. These invisible comet tails slow down individual particles, greatly increasing their residence time. Based on these findings, we constructed a reduced-order model for the Stokesian sedimentation of these mucus-embedded two-phase particles, paving the way toward a predictive understanding of marine snow.

  View details for DOI 10.1126/science.adl5767

  View details for PubMedID 39388567

• Escape motility of multicellular magnetotactic prokaryotes. Journal of the Royal Society, Interface Yang, X., Prakash, M., Brumley, D. R. 2024; 21 (219): 20240310

  Abstract

  Microorganisms often actively respond to multiple external stimuli to navigate toward their preferred niches. For example, unicellular magnetotactic bacteria integrate both oxygen sensory information and the Earth's geomagnetic field to help them locate anoxic conditions in a process known as magneto-aerotaxis. However, for multicellular magnetotactic prokaryotes (MMPs), the colonial structure of 4-16 cells places fundamental constraints on collective sensing, colony motility and directed swimming. To investigate how colonies navigate environments with multiple stimuli, we performed microfluidic experiments of MMPs with opposing magnetic fields and oxygen gradients. These experiments reveal unusual back-and-forth excursions called 'escape motility', in which colonies shuttle along magnetic field lines, punctuated by abrupt-yet highly coordinated-changes in collective ciliary beating. Through cell tracking and numerical simulations, we demonstrate that escape motility can arise through a simple magneto-aerotaxis mechanism, which includes the effect of magnetic torques and chemical sensing. At sufficiently high densities of MMPs, we observe the formation of dynamic crystal structures, whose stability is governed by the magnetic field strength and near-field hydrodynamic interactions. The results shed light on how some of the earliest multicellular organisms navigate complex physico-chemical landscapes.

  View details for DOI 10.1098/rsif.2024.0310

  View details for PubMedID 39410817

  View details for PubMedCentralID PMC11480751

• Split Luciferase Molecular Tension Sensors for Bioluminescent Readout of Mechanical Forces in Biological Systems. ACS sensors Zhong, B. L., Elliot, J. M., Wang, P., Li, H., Hall, R. N., Wang, B., Prakash, M., Dunn, A. R. 2024

  Abstract

  The ability of proteins to sense and transmit mechanical forces underlies many biological processes, but characterizing these forces in biological systems remains a challenge. Existing genetically encoded force sensors typically rely on fluorescence or bioluminescence resonance energy transfer (FRET or BRET) to visualize tension. However, these force sensing modules are relatively large, and interpreting measurements requires specialized image analysis and careful control experiments. Here, we report a compact molecular tension sensor that generates a bioluminescent signal in response to tension. This sensor (termed PILATeS) makes use of the split NanoLuc luciferase and consists of the H. sapiens titin I10 domain with the insertion of a 10-15 amino acid tag derived from the C-terminal β-strand of NanoLuc. Mechanical load across PILATeS mediates exposure of this tag to recruit the complementary split NanoLuc fragment, resulting in force-dependent bioluminescence. We demonstrate the ability of PILATeS to report biologically meaningful forces by visualizing forces at the interface between integrins and extracellular matrix substrates. We further use PILATeS as a genetically encoded sensor of tension experienced by the mechanosensing protein vinculin. We anticipate that PILATeS will provide an accessible means of visualizing molecular-scale forces in biological systems.

  View details for DOI 10.1021/acssensors.3c02664

  View details for PubMedID 38973210

• Droplet tilings in precessive fields: hysteresis, elastic defects, and annealing. Soft matter Molina, A., Prakash, M. 2024

  Abstract

  Two-component Marangoni contracted droplets can be arranged into arbitrary two-dimensional tiling patterns where they display rich dynamics due to vapor-mediated long-range interactions. Recent work has characterized the centered hexagonal honeycomb lattice, showing it to be a highly frustrated system with many metastable states and relaxation occurring over multiple timescales [Molina et al., Proc. Natl. Acad. Sci. U. S. A., 2021, 118, e2020014118]. Here, we study this system under the influence of a rotating gravitational field. High amplitudes are able to completely disrupt droplet-droplet interactions, making it possible to identify a transition between field-dominated and interaction-dominated regimes. The system displays complex hysteresis behavior, the details of which are connected to the emergence of linear mesoscale structures. These mesoscale features display an elasticity that is governed by the balance between gravity and long-range vapor-mediated attractions. We find that disorder plays an important role in determining the dynamics of these features. Finally, we demonstrate annealing the system by progressively reducing the field amplitude, a process that reduces configurational energy compared to a rapid quench. The ability to manipulate vapor-mediated interactions in deliberately designed droplet tilings provides a novel platform for table-top explorations of multi-body interactions.

  View details for DOI 10.1039/d4sm00475b

  View details for PubMedID 38922641

• Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Ogunlade, B., Tadesse, L. F., Li, H., Vu, N., Banaei, N., Barczak, A. K., Saleh, A. A., Prakash, M., Dionne, J. A. 2024; 121 (25): e2315670121

  Abstract

  Tuberculosis (TB) is the world's deadliest infectious disease, with over 1.5 million deaths and 10 million new cases reported anually. The causative organism Mycobacterium tuberculosis (Mtb) can take nearly 40 d to culture, a required step to determine the pathogen's antibiotic susceptibility. Both rapid identification and rapid antibiotic susceptibility testing of Mtb are essential for effective patient treatment and combating antimicrobial resistance. Here, we demonstrate a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for TB using Raman spectroscopy and machine learning. We collect few-to-single-cell Raman spectra from over 25,000 cells of the Mtb complex strain Bacillus Calmette-Guérin (BCG) resistant to one of the four mainstay anti-TB drugs, isoniazid, rifampicin, moxifloxacin, and amikacin, as well as a pan-susceptible wildtype strain. By training a neural network on this data, we classify the antibiotic resistance profile of each strain, both on dried samples and on patient sputum samples. On dried samples, we achieve >98% resistant versus susceptible classification accuracy across all five BCG strains. In patient sputum samples, we achieve ~79% average classification accuracy. We develop a feature recognition algorithm in order to verify that our machine learning model is using biologically relevant spectral features to assess the resistance profiles of our mycobacterial strains. Finally, we demonstrate how this approach can be deployed in resource-limited settings by developing a low-cost, portable Raman microscope that costs <$5,000. We show how this instrument and our machine learning model enable combined microscopy and spectroscopy for accurate few-to-single-cell drug susceptibility testing of BCG.

  View details for DOI 10.1073/pnas.2315670121

  View details for PubMedID 38861604

• Curved crease origami and topological singularities enable hyperextensibility ofL. olor. Science (New York, N.Y.) Flaum, E., Prakash, M. 2024; 384 (6700): eadk5511

  Abstract

  Fundamental limits of cellular deformations, such as hyperextension of a living cell, remain poorly understood. Here, we describe how the single-celled protist Lacrymaria olor, a 40-micrometer cell, is capable of reversibly and repeatably extending its necklike protrusion up to 1200 micrometers in 30 seconds. We discovered a layered cortical cytoskeleton and membrane architecture that enables hyperextensions through the folding and unfolding of cellular-scale origami. Physical models of this curved crease origami display topological singularities, including traveling developable cones and cytoskeletal twisted domain walls, which provide geometric control of hyperextension. Our work unravels how cell geometry encodes behavior in single cells and provides inspiration for geometric control in microrobotics and deployable architectures.

  View details for DOI 10.1126/science.adk5511

  View details for PubMedID 38843314

• Coupling and uncoupling of midline morphogenesis and cell flow in amniote gastrulation. eLife Asai, R., Prakash, V. N., Sinha, S., Prakash, M., Mikawa, T. 2024; 12

  Abstract

  Large-scale cell flow characterizes gastrulation in animal development. In amniote gastrulation, particularly in avian gastrula, a bilateral vortex-like counter-rotating cell flow, called 'polonaise movements', appears along the midline. Here, through experimental manipulations, we addressed relationships between the polonaise movements and morphogenesis of the primitive streak, the earliest midline structure in amniotes. Suppression of the Wnt/planar cell polarity (PCP) signaling pathway maintains the polonaise movements along a deformed primitive streak. Mitotic arrest leads to diminished extension and development of the primitive streak and maintains the early phase of the polonaise movements. Ectopically induced Vg1, an axis-inducing morphogen, generates the polonaise movements, aligned to the induced midline, but disturbs the stereotypical cell flow pattern at the authentic midline. Despite the altered cell flow, induction and extension of the primitive streak are preserved along both authentic and induced midlines. Finally, we show that ectopic axis-inducing morphogen, Vg1, is capable of initiating the polonaise movements without concomitant PS extension under mitotic arrest conditions. These results are consistent with a model wherein primitive streak morphogenesis is required for the maintenance of the polonaise movements, but the polonaise movements are not necessarily responsible for primitive streak morphogenesis. Our data describe a previously undefined relationship between the large-scale cell flow and midline morphogenesis in gastrulation.

  View details for DOI 10.7554/eLife.89948

  View details for PubMedID 38727576

• Energetics of the microsporidian polar tube invasion machinery. eLife Chang, R., Davydov, A., Jaroenlak, P., Budaitis, B., Ekiert, D. C., Bhabha, G., Prakash, M. 2024; 12

  Abstract

  Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an unusual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive. Anncaliia algerae microsporidia spores (3-4 μm in size) shoot out a 100-nm-wide PT at a speed of 300 μm/s, creating a shear rate of 3000 s-1. The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ∼60-140 μm (Jaroenlak et al, 2020) and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots of A. algerae spores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT firing experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.

  View details for DOI 10.7554/eLife.86638

  View details for PubMedID 38381133

  View details for PubMedCentralID PMC10942582

• Mechanopathology of biofilm-like Mycobacterium tuberculosis cords. Cell Mishra, R., Hannebelle, M., Patil, V. P., Dubois, A., Garcia-Mouton, C., Kirsch, G. M., Jan, M., Sharma, K., Guex, N., Sordet-Dessimoz, J., Perez-Gil, J., Prakash, M., Knott, G. W., Dhar, N., McKinney, J. D., Thacker, V. V. 2023

  Abstract

  Mycobacterium tuberculosis (Mtb) cultured axenically without detergent forms biofilm-like cords, a clinical identifier of virulence. In lung-on-chip (LoC) and mouse models, cords in alveolar cells contribute to suppression of innate immune signaling via nuclear compression. Thereafter, extracellular cords cause contact-dependent phagocyte death but grow intercellularly between epithelial cells. The absence of these mechanopathological mechanisms explains the greater proportion of alveolar lesions with increased immune infiltration and dissemination defects in cording-deficient Mtb infections. Compression of Mtb lipid monolayers induces a phase transition that enables mechanical energy storage. Agent-based simulations demonstrate that the increased energy storage capacity is sufficient for the formation of cords that maintain structural integrity despite mechanical perturbation. Bacteria in cords remain translationally active despite antibiotic exposure and regrow rapidly upon cessation of treatment. This study provides a conceptual framework for the biophysics and function in tuberculosis infection and therapy of cord architectures independent of mechanisms ascribed to single bacteria.

  View details for DOI 10.1016/j.cell.2023.09.016

  View details for PubMedID 37865090

• Topological damping in an ultrafast giant cell. Proceedings of the National Academy of Sciences of the United States of America Chang, R., Prakash, M. 2023; 120 (41): e2303940120

  Abstract

  Cellular systems are known to exhibit some of the fastest movements in biology, but little is known as to how single cells can dissipate this energy rapidly and adapt to such large accelerations without disrupting internal architecture. To address this, we investigate Spirostomum ambiguum-a giant cell (1-4 mm in length) well-known to exhibit ultrafast contractions (50% of body length) within 5 ms with a peak acceleration of 15[Formula: see text]. Utilizing transmitted electron microscopy and confocal imaging, we identify an association of rough endoplasmic reticulum (RER) and vacuoles throughout the cell-forming a contiguous fenestrated membrane architecture that topologically entangles these two organelles. A nearly uniform interorganelle spacing of 60 nm is observed between RER and vacuoles, closely packing the entire cell. Inspired by the entangled organelle structure, we study the mechanical properties of entangled deformable particles using a vertex-based model, with all simulation parameters matching 10 dimensionless numbers to ensure dynamic similarity. We demonstrate how entangled deformable particles respond to external loads by an increased viscosity against squeezing and help preserve spatial relationships. Because this enhanced damping arises from the entanglement of two networks incurring a strain-induced jamming transition at subcritical volume fractions, which is demonstrated through the spatial correlation of velocity direction, we term this phenomenon "topological damping." Our findings suggest a mechanical role of RER-vacuolar meshwork as a metamaterial capable of damping an ultrafast contraction event.

  View details for DOI 10.1073/pnas.2303940120

  View details for PubMedID 37792511

• Thermotaxis in an apolar, non-neuronal animal. Journal of the Royal Society, Interface Zhong, G., Kroo, L., Prakash, M. 2023; 20 (206): 20230279

  Abstract

  Neuronal circuits are hallmarks of complex decision-making processes in the animal world. How animals without neurons process information and respond to environmental cues promises a new window into studying precursors of neuronal control and origin of the nervous system as we know it today. Robust decision making in animals, such as in chemotaxis or thermotaxis, often requires internal symmetry breaking (such as anterior-posterior (AP) axis) provided naturally by a given body plan of an animal. Here we report the discovery of robust thermotaxis behaviour in Trichoplax adhaerens, an early-divergent, enigmatic animal with no anterior-posterior symmetry breaking (apolar) and no known neurons or muscles. We present a quantitative and robust behavioural response assay in Placozoa, which presents an apolar flat geometry. By exposing T. adhaerens to a thermal gradient under a long-term imaging set-up, we observe robust thermotaxis that occurs over timescale of hours, independent of any circadian rhythms. We quantify that T. adhaerens can detect thermal gradients of at least 0.1°C cm-1. Positive thermotaxis is observed for a range of baseline temperatures from 17°C to 22.5°C, and distributions of momentary speeds for both thermotaxis and control conditions are well described by single exponential fits. Interestingly, the organism does not maintain a fixed orientation while performing thermotaxis. Using natural diversity in size of adult organisms (100 µm to a few millimetres), we find no apparent size-dependence in thermotaxis behaviour across an order of magnitude of organism size. Several transient receptor potential (TRP) family homologues have been previously reported to be conserved in metazoans, including in T. adhaerens. We discover naringenin, a known TRPM3 antagonist, inhibits thermotaxis in T. adhaerens. The discovery of robust thermotaxis in T. adhaerens provides a tractable handle to interrogate information processing in a brainless animal. Understanding how divergent marine animals process thermal cues is also critical due to rapid temperature rise in our oceans.

  View details for DOI 10.1098/rsif.2023.0279

  View details for PubMedID 37700707

• Curved crease origami and topological singularities at a cellular scale enable hyper-extensibility of Lacrymaria olor. bioRxiv : the preprint server for biology Flaum, E., Prakash, M. 2023

  Abstract

  Eukaryotic cells undergo dramatic morphological changes during cell division, phagocytosis and motility. Fundamental limits of cellular morphodynamics such as how fast or how much cellular shapes can change without harm to a living cell remain poorly understood. Here we describe hyper-extensibility in the single-celled protist Lacrymaria olor , a 40 m cell which is capable of reversible and repeatable extensions (neck-like protrusions) up to 1500 m in 30 seconds. We discover that a unique and intricate organization of cortical cytoskeleton and membrane enables these hyper-extensions that can be described as the first cellular scale curved crease origami. Furthermore, we show how these topological singularities including d- cones and twisted domain walls provide a geometrical control mechanism for the deployment of membrane and microtubule sheets as they repeatably spool thousands of time from the cell body. We lastly build physical origami models to understand how these topological singularities provide a mechanism for the cell to control the hyper-extensile deployable structure. This new geometrical motif where a cell employs curved crease origami to perform a physiological function has wide ranging implications in understanding cellular morphodynamics and direct applications in deployable micro-robotics.Significance statement: Here we present the discovery of curved crease origami at the scale of a single cell. We show how topological singularities in the origami (d-cones) and twist walls in microtubule ribbons control deployment of a hyper-extensile neck in a single-celled protist. Our work establishes a direct link between geometry and cell behavior, connecting form and function of cellular morphodynamics.

  View details for DOI 10.1101/2023.08.04.551915

  View details for PubMedID 37577489

• Culture-Independent Multiplexed Detection of Drug-Resistant Bacteria Using Surface-Enhanced Raman Scattering. ACS sensors Dai, T., Xiao, Z., Shan, D., Moreno, A., Li, H., Prakash, M., Banaei, N., Rao, J. 2023

  Abstract

  The rapid and accurate detection of bacteria resistance to β-lactam antibiotics is critical to inform optimal treatment and prevent overprescription of potent antibiotics. Here, we present a fast, culture-independent method for the detection of extended-spectrum β-lactamases (ESBLs) using surface-enhanced Raman scattering (SERS). The method uses Raman probes that release sulfur-based Raman active molecules in the presence of β-lactamases. The released thiol molecules can be captured by gold nanoparticles, leading to amplified Raman signals. A broad-spectrum cephalosporin probe R1G and an ESBL-specific probe R3G are designed to enable duplex detection of bacteria expressing broad-spectrum β-lactamases or ESBLs with a detection limit of 103 cfu/mL in 1 h incubation. Combined with a portable Raman microscope, our culturing-free SERS assay has reduced screening time to 1.5 h without compromising sensitivity and specificity.

  View details for DOI 10.1021/acssensors.3c01345

  View details for PubMedID 37506677

• Emergent programmable behavior and chaos in dynamically driven active filaments. Proceedings of the National Academy of Sciences of the United States of America Krishnamurthy, D., Prakash, M. 2023; 120 (28): e2304981120

  Abstract

  How the behavior of cells emerges from their constituent subcellular biochemical and physical parts is an outstanding challenge at the intersection of biology and physics. A remarkable example of single-cell behavior occurs in the ciliate Lacrymaria olor, which hunts for its prey via rapid movements and protrusions of a slender neck, many times the size of the original cell body. The dynamics of this cell neck is powered by a coat of cilia across its length and tip. How a cell can program this active filamentous structure to produce desirable behaviors like search and homing to a target remains unknown. Here, we present an active filament model that allows us to uncover how a "program" (time sequence of active forcing) leads to "behavior" (filament shape dynamics). Our model captures two key features of this system-time-varying activity patterns (extension and compression cycles) and active stresses that are uniquely aligned with the filament geometry-a "follower force" constraint. We show that active filaments under deterministic, time-varying follower forces display rich behaviors including periodic and aperiodic dynamics over long times. We further show that aperiodicity occurs due to a transition to chaos in regions of a biologically accessible parameter space. We also identify a simple nonlinear iterated map of filament shape that approximately predicts long-term behavior suggesting simple, artificial "programs" for filament functions such as homing and searching space. Last, we directly measure the statistical properties of biological programs in L. olor, enabling comparisons between model predictions and experiments.

  View details for DOI 10.1073/pnas.2304981120

  View details for PubMedID 37406100

• Predicting tuberculosis drug resistance with machine learning-assisted Raman spectroscopy. ArXiv Ogunlade, B., Tadesse, L. F., Li, H., Vu, N., Banaei, N., Barczak, A. K., Saleh, A. A., Prakash, M., Dionne, J. A. 2023

  Abstract

  Tuberculosis (TB) is the world's deadliest infectious disease, with 1.5 million annual deaths and half a million annual infections. Rapid TB diagnosis and antibiotic susceptibility testing (AST) are critical to improve patient treatment and to reduce the rise of new drug resistance. Here, we develop a rapid, label-free approach to identify Mycobacterium tuberculosis (Mtb) strains and antibiotic-resistant mutants. We collect over 20,000 single-cell Raman spectra from isogenic mycobacterial strains each resistant to one of the four mainstay anti-TB drugs (isoniazid, rifampicin, moxifloxacin and amikacin) and train a machine-learning model on these spectra. On dried TB samples, we achieve > 98% classification accuracy of the antibiotic resistance profile, without the need for antibiotic co-incubation; in dried patient sputum, we achieve average classification accuracies of ~ 79%. We also develop a low-cost, portable Raman microscope suitable for field-deployment of this method in TB-endemic regions.

  View details for DOI 10.3390/molecules24244516

  View details for PubMedID 37332564

  View details for PubMedCentralID PMC10274949

• Coupling and uncoupling of midline morphogenesis and cell flow in amniote gastrulation. bioRxiv : the preprint server for biology Asai, R., Prakash, V. N., Sinha, S., Prakash, M., Mikawa, T. 2023

  Abstract

  Large-scale cell flow characterizes gastrulation in animal development. In amniote gastrulation, a bilateral vortex-like counter-rotating cell flow, called 'polonaise movements', appears along the midline. Here, through experimental manipulations, we addressed relationships between the polonaise movements and morphogenesis of the primitive streak, the earliest midline structure in amniotes. Suppression of the Wnt/planar cell polarity (PCP) signaling pathway maintains the polonaise movements along a deformed primitive streak. Mitotic arrest leads to diminished extension and development of the primitive streak and maintains the early phase of the polonaise movements. Ectopically induced Vg1, an axis-inducing morphogen, generates the polonaise movements, aligned to the induced midline, but disturbs the stereotypical cell flow pattern at the authentic midline. Despite the altered cell flow, induction and extension of the primitive streak are preserved along both authentic and induced midlines. Finally, we show that ectopic axis-inducing morphogen, Vg1, is capable of initiating the polonaise movements without concomitant PS extension under mitotic arrest conditions. These results are consistent with a model wherein primitive streak morphogenesis is required for the maintenance of the polonaise movements, but the polonaise movements are not necessarily responsible for primitive streak morphogenesis. Our data describe a previously undefined relationship between the large-scale cell flow and midline morphogenesis in gastrulation.

  View details for DOI 10.1101/2023.05.26.542486

  View details for PubMedID 37293063

• MultiSero: An Open-Source Multiplex-ELISA Platform for Measuring Antibody Responses to Infection. Pathogens (Basel, Switzerland) Byrum, J. R., Waltari, E., Janson, O., Guo, S., Folkesson, J., Chhun, B. B., Vinden, J., Ivanov, I. E., Forst, M. L., Li, H., Larson, A. G., Blackmon, L., Liu, Z., Wu, W., Ahyong, V., Tato, C. M., McCutcheon, K. M., Hoh, R., Kelly, J. D., Martin, J. N., Peluso, M. J., Henrich, T. J., Deeks, S. G., Prakash, M., Greenhouse, B., Mehta, S. B., Pak, J. E. 2023; 12 (5)

  Abstract

  A multiplexed enzyme-linked immunosorbent assay (ELISA) that simultaneously measures antibody binding to multiple antigens can extend the impact of serosurveillance studies, particularly if the assay approaches the simplicity, robustness, and accuracy of a conventional single-antigen ELISA. Here, we report on the development of multiSero, an open-source multiplex ELISA platform for measuring antibody responses to viral infection. Our assay consists of three parts: (1) an ELISA against an array of proteins in a 96-well format; (2) automated imaging of each well of the ELISA array using an open-source plate reader; and (3) automated measurement of optical densities for each protein within the array using an open-source analysis pipeline. We validated the platform by comparing antibody binding to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens in 217 human sera samples, showing high sensitivity (0.978), specificity (0.977), positive predictive value (0.978), and negative predictive value (0.977) for classifying seropositivity, a high correlation of multiSero determined antibody titers with commercially available SARS-CoV-2 antibody tests, and antigen-specific changes in antibody titer dynamics upon vaccination. The open-source format and accessibility of our multiSero platform can contribute to the adoption of multiplexed ELISA arrays for serosurveillance studies, for SARS-CoV-2 and other pathogens of significance.

  View details for DOI 10.3390/pathogens12050671

  View details for PubMedID 37242341

• Active foam: the adaptive mechanics of 2D air-liquid foam under cyclic inflation. Soft matter Kroo, L. A., Bull, M. S., Prakash, M. 2023

  Abstract

  Foam is a canonical example of disordered soft matter where local force balance leads to the competition of many metastable configurations. We present an experimental and theoretical framework for "active foam" where an individual voxel inflates and deflates periodically. Local periodic activity leads to irreversible and reversible T1 transitions throughout the foam, eventually reaching a reversible limit cycle. Individual vertices displace outwards and subsequently return back to their approximate original radial position; this radial displacement follows an inverse law. Surprisingly, each return trajectory does not retrace its outbound path but encloses a finite area, with a clockwise (CW) or counterclockwise (CCW) direction, which we define as a local swirl. These swirls form coherent patterns spanning the scale of the material. Using a dynamical model, we demonstrate that swirl arises from disorder in the local micro-structure. We demonstrate that disorder and strain-rate control a crossover between cooperation and competition between swirls in adjacent vertices. Over 5-10 cycles, the region around the active voxel structurally adapts from a higher-energy metastable state to a lower-energy state, locally ordering and stiffening the structure. The coherent domains of CW/CCW swirl become smaller as the system stabilizes, indicative of a process similar to the Hall-Petch effect. Finally, we introduce a statistical model that evolves edge lengths with a set of rules to explore how this class of materials adapts as a function of initial structure. Adding activity to foam couples structural disorder and adaptive dynamics to encourage the development of a new class of abiotic, cellularized active matter.

  View details for DOI 10.1039/d3sm00019b

  View details for PubMedID 36942719

• Effect of age on wingbeat frequency of Aedes aegypti and potential application for age estimation of mosquitoes. Medical and veterinary entomology Park, D., Bowles, J., Norrid, K., Dobson, F. S., Abebe, A., Narayanan, H. V., Prakash, M., Blagburn, B., Starkey, L., Zohdy, S. 2023

  Abstract

  To combat mosquito-borne diseases, a variety of vector control tools have been implemented. Estimating age structure in populations of vector species is important for understanding transmission potential. Age-grading techniques have been used as critical methods for evaluating the efficacy of vector control tools. However, methods like mark-release-recapture and ovarian dissection are laborious and require a high level of training. For decades, scientists have discussed the wide array of acoustic signatures of different mosquito species. These distinguishable wingbeat signatures with spatiotemporal classification allow mosquitoes of the same species to locate one another for mating. In recent years, the use of sensitive acoustic devices like mobile phones have proved effective. Wingbeat signatures can be used to identify mosquito species without the challenge of intensive field collections and morphological and molecular identifications. In this study, laboratory Aedes aegypti (L.) female and male wingbeats were recorded using mobile phones to determine whether sex and age differences with chronological time, and across different physiological stages, can be detected. Our results indicate significantly different wingbeat signatures between male and female Ae. aegypti, and a change of wingbeat frequencies with age and reproduction stage in females.

  View details for DOI 10.1111/mve.12647

  View details for PubMedID 36872598

• Active sinking particles: sessile suspension feeders significantly alter the flow and transport to sinking aggregates. Journal of the Royal Society, Interface Krishnamurthy, D., Pepper, R., Prakash, M. 2023; 20 (199): 20220537

  Abstract

  Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in wastewater treatment plants. In both these contexts, the sinking aggregates are 'active', since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories and mass transfer to these 'active sinking particles' has not previously been studied. Here, we use a novel scale-free vertical tracking microscope (a.k.a. gravity machine; Krishnamurthy et al. 2020 Nat. Methods 17, 1040-1051 (doi:10.1038/s41592-020-0924-7)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached V. convallaria causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall, our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes.

  View details for DOI 10.1098/rsif.2022.0537

  View details for PubMedID 36751929

• Energetics of the Microsporidian Polar Tube Invasion Machinery. bioRxiv : the preprint server for biology Chang, R., Davydov, A., Jaroenlak, P., Budaitis, B., Ekiert, D. C., Bhabha, G., Prakash, M. 2023

  Abstract

  Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an un-usual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive. Anncaliia algerae microsporidia spores (3-4 mu m in size) shoot out a 100-nm-wide PT at a speed of 300 mu m/sec, creating a shear rate of 3000 sec - 1 . The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ~60-140 mu m 1 and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots of A. algerae spores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT firing experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement, pressure and power. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.Statement of Significance: Microsporidia are a group of spore-forming, intracellular parasites that infect a wide range of hosts (including humans). Once triggered, microsporidian spores (3-4 mu m in size) shoot out a specialized organelle called the polar tube (PT) (60-140 mu m long, 100 nm wide) at ultrafast speed (300 mu m/sec), penetrating host cells and acting as a conduit for the transport of infectious cargo. Although this process has fascinated biologists for a century, the biophysical mechanisms underlying PT extrusion are not understood. We thus take a data-driven approach to generate models for the physical basis of PT firing and cargo transport through the PT. Our approach here demonstrates the extreme limits of cellular hydraulics and the potential applications of biophysical approaches to other cellular architectures.

  View details for DOI 10.1101/2023.01.17.524456

  View details for PubMedID 36711805

• Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale FRONTIERS IN MARINE SCIENCE de Vargas, C., Le Bescot, N., Pollina, T., Henry, N., Romac, S., Colin, S., Haentjens, N., Carmichael, M., Berger, C., Le Guen, D., Decelle, J., Mahe, F., Poulain, J., Malpot, E., Beaumont, C., Hardy, M., Guiffant, D., Probert, I., Gruber, D. F., Allen, A. E., Gorsky, G., Follows, M. J., Pochon, X., Trouble, R., Cael, B. B., Lombard, F., Boss, E., Prakash, M., Plankton Planet Core Team 2022; 9

  View details for DOI 10.3389/fmars.2022.936972

  View details for Web of Science ID 000848152100001

• PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography FRONTIERS IN MARINE SCIENCE Pollina, T., Larson, A. G., Lombard, F., Li, H., Le Guen, D., Colin, S., de Vargas, C., Prakash, M. 2022; 9

  View details for DOI 10.3389/fmars.2022.949428

  View details for Web of Science ID 000837418200001

• Basin-Scale Underway Quantitative Survey of Surface Microplankton Using Affordable Collection and Imaging Tools Deployed From Tara FRONTIERS IN MARINE SCIENCE Meriguet, Z., Oddone, A., Le Guen, D., Pollina, T., Bazile, R., Moulin, C., Trouble, R., Prakash, M., de Vargas, C., Lombard, F. 2022; 9

  View details for DOI 10.3389/fmars.2022.916025

  View details for Web of Science ID 000828778200001

• A freely suspended robotic swimmer propelled by viscoelastic normal stresses JOURNAL OF FLUID MECHANICS Kroo, L. A., Binagia, J. P., Eckman, N., Prakash, M., Shaqfeh, E. S. G. 2022; 944

  View details for DOI 10.1017/jfm.2022.485

  View details for Web of Science ID 000817205500001

• Low cost centrifugal melt spinning for distributed manufacturing of non-woven media. PloS one Molina, A., Vyas, P., Khlystov, N., Kumar, S., Kothari, A., Deriso, D., Liu, Z., Banavar, S., Flaum, E., Prakash, M. 2022; 17 (4): e0264933

  Abstract

  Centralized manufacturing and global supply chains have emerged as an efficient strategy for large-scale production of goods throughout the 20th century. However, while this system of production is highly efficient, it is not resilient. The COVID-19 pandemic has seen numerous supply chains fail to adapt to sudden changes in supply and demand, including those for goods critical to the pandemic response such as personal protective equipment. Here, we consider the production of the non-woven polypropylene filtration media used in face filtering respirators (FFRs). The FFR supply chain's reliance on non-woven media sourced from large, centralized manufacturing facilities led to a supply chain failure. In this study, we present an alternative manufacturing strategy that allows us to move towards a more distributed manufacturing practice that is both scalable and robust. Specifically, we demonstrate that a fiber production technique known as centrifugal melt spinning can be implemented with modified, commercially-available cotton candy machines to produce nano- and microscale non-woven fibers. We evaluate several post processing strategies to transform the produced material into viable filtration media and then characterize these materials by measuring filtration efficiency and breathability, comparing them against equivalent materials used in commercially-available FFRs. Additionally, we demonstrate that waste plastic can be processed with this technique, enabling the development of distributed recycling strategies to address the growing plastic waste crisis. Since this method can be employed at small scales, it allows for the development of an adaptable and rapidly deployable distributed manufacturing network for non-woven materials that is financially accessible to more people than is currently possible.

  View details for DOI 10.1371/journal.pone.0264933

  View details for PubMedID 35439249

• Engineering reconfigurable flow patterns via surface-driven light-controlled active matter PHYSICAL REVIEW FLUIDS Gong, X., Mathijssen, A. M., Bryant, Z., Prakash, M. 2021; 6 (12)

  View details for DOI 10.1103/PhysRevFluids.6.123104

  View details for Web of Science ID 000739637100001

• A microfluidic platform for highly parallel bite by bite profiling of mosquito-borne pathogen transmission. Nature communications Kumar, S., Hol, F. J., Pujhari, S., Ellington, C., Narayanan, H. V., Li, H., Rasgon, J. L., Prakash, M. 2021; 12 (1): 6018

  Abstract

  Mosquito bites transmit a number of pathogens via salivary droplets deposited during blood-feeding, resulting in potentially fatal diseases. Little is known about the genomic content of these nanodroplets, including the transmission dynamics of live pathogens. Here we introduce Vectorchip, a low-cost, scalable microfluidic platform enabling high-throughput molecular interrogation of individual mosquito bites. We introduce an ultra-thin PDMS membrane which acts as a biting interface to arrays of micro-wells. Freely-behaving mosquitoes deposit saliva droplets by biting into these micro-wells. By modulating membrane thickness, we observe species-dependent differences in mosquito biting capacity, utilizable for selective sample collection. We demonstrate RT-PCR and focus-forming assays on-chip to detect mosquito DNA, Zika virus RNA, as well as quantify infectious Mayaro virus particles transmitted from single mosquito bites. The Vectorchip presents a promising approach for single-bite-resolution laboratory and field characterization of vector-pathogen communities, and could serve as a powerful early warning sentinel for mosquito-borne diseases.

  View details for DOI 10.1038/s41467-021-26300-0

  View details for PubMedID 34650045

• Modeling epithelial tissues as active-elastic sheets reproduce contraction pulses and predict rip resistance COMMUNICATIONS PHYSICS Armon, S., Bull, M. S., Moriel, A., Aharoni, H., Prakash, M. 2021; 4 (1)

  View details for DOI 10.1038/s42005-021-00712-2

  View details for Web of Science ID 000698699300002

• Droplet tilings for rapid exploration of spatially constrained many-body systems. Proceedings of the National Academy of Sciences of the United States of America Molina, A., Kumar, S., Karpitschka, S., Prakash, M. 2021; 118 (34)

  Abstract

  Geometry in materials is a key concept which can determine material behavior in ordering, frustration, and fragmentation. More specifically, the behavior of interacting degrees of freedom subject to arbitrary geometric constraints has the potential to be used for engineering materials with exotic phase behavior. While advances in lithography have allowed for an experimental exploration of geometry on ordering that has no precedent in nature, many of these methods are low throughput or the underlying dynamics remain difficult to observe directly. Here, we introduce an experimental system that enables the study of interacting many-body dynamics by exploiting the physics of multidroplet evaporation subject to two-dimensional spatial constraints. We find that a high-energy initial state of this system settles into frustrated, metastable states with relaxation on two timescales. We understand this process using a minimal dynamical model that simulates the overdamped dynamics of motile droplets by identifying the force exerted on a given droplet as being proportional to the two-dimensional vapor gradients established by its neighbors. Finally, we demonstrate the flexibility of this platform by presenting experimental realizations of droplet-lattice systems representing different spin degrees of freedom and lattice geometries. Our platform enables a rapid and low-cost means to directly visualize dynamics associated with complex many-body systems interacting via long-range interactions. More generally, this platform opens up the rich design space between geometry and interactions for rapid exploration with minimal resources.

  View details for DOI 10.1073/pnas.2020014118

  View details for PubMedID 34417307

• Choosing Wisely for COVID-19: ten evidence-based recommendations for patients and physicians. Nature medicine Pramesh, C. S., Babu, G. R., Basu, J., Bhushan, I., Booth, C. M., Chinnaswamy, G., Guleria, R., Kalantri, S. P., Kang, G., Mohan, P., Mor, N., Pai, M., Prakash, M., Rupali, P., Sampathkumar, P., Sengar, M., Sullivan, R., Ranganathan, P. 2021

  View details for DOI 10.1038/s41591-021-01439-x

  View details for PubMedID 34226738

• India's COVID-19 crisis: a call for international action. Lancet (London, England) Kuppalli, K., Gala, P., Cherabuddi, K., Kalantri, S. P., Mohanan, M., Mukherjee, B., Pinto, L., Prakash, M., Pramesh, C. S., Rathi, S., Pai, N. P., Yamey, G., Pai, M. 2021

  View details for DOI 10.1016/S0140-6736(21)01121-1

  View details for PubMedID 34000256

• multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection. medRxiv : the preprint server for health sciences Byrum, J. R., Waltari, E., Janson, O., Guo, S. M., Folkesson, J., Chhun, B. B., Vinden, J., Ivanov, I. E., Forst, M. L., Li, H., Larson, A. G., Wu, W., Tato, C. M., McCutcheon, K. M., Peluso, M. J., Henrich, T. J., Deeks, S. G., Prakash, M., Greenhouse, B., Pak, J. E., Mehta, S. B. 2021

  Abstract

  Serology has provided valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 in diverse patient cohorts. Deployment of high content, multiplex serology platforms across the world, including in low and medium income countries, can accelerate longitudinal epidemiological surveys. Here we report multiSero, an open platform to enable multiplex serology with up to 48 antigens in a 96-well format. The platform consists of three components: ELISA-array of printed proteins, a commercial or home-built plate reader, and modular python software for automated analysis (pysero). We validate the platform by comparing antibody titers against the SARS-CoV-2 Spike, receptor binding domain (RBD), and nucleocapsid (N) in 114 sera from COVID-19 positive individuals and 87 pre-pandemic COVID-19 negative sera. We report data with both a commercial plate reader and an inexpensive, open plate reader (nautilus). Receiver operating characteristic (ROC) analysis of classification with single antigens shows that Spike and RBD classify positive and negative sera with the highest sensitivity at a given specificity. The platform distinguished positive sera from negative sera when the reactivity of the sera was equivalent to the binding of 1 ng mL âˆ'1 RBD-specific monoclonal antibody. We developed normalization and classification methods to pool antibody responses from multiple antigens and multiple experiments. Our results demonstrate a performant and accessible pipeline for multiplexed ELISA ready for multiple applications, including serosurveillance, identification of viral proteins that elicit antibody responses, differential diagnosis of circulating pathogens, and immune responses to vaccines.

  View details for DOI 10.1101/2021.05.07.21249238

  View details for PubMedID 34013298

  View details for PubMedCentralID PMC8132273

• Motility-induced fracture reveals a ductile-to-brittle crossover in a simple animal's epithelia NATURE PHYSICS Prakash, V. N., Bull, M. S., Prakash, M. 2021

  View details for DOI 10.1038/s41567-020-01134-7

  View details for Web of Science ID 000608659800003

• Modified full-face snorkel masks as reusable personal protective equipment for hospital personnel. PloS one Kroo, L., Kothari, A., Hannebelle, M., Herring, G., Pollina, T., Chang, R., Peralta, D., Banavar, S. P., Flaum, E., Soto-Montoya, H., Li, H., Combes, K., Pan, E., Vu, K., Yen, K., Dale, J., Kolbay, P., Ellgas, S., Konte, R., Hajian, R., Zhong, G., Jacobs, N., Jain, A., Kober, F., Ayala, G., Allinne, Q., Cucinelli, N., Kasper, D., Borroni, L., Gerber, P., Venook, R., Baek, P., Arora, N., Wagner, P., Miki, R., Kohn, J., Kohn Bitran, D., Pearson, J., Arias-Arco, B., Larrainzar-Garijo, R., Herrera, C. M., Prakash, M. 2021; 16 (1): e0244422

  Abstract

  Here we adapt and evaluate a full-face snorkel mask for use as personal protective equipment (PPE) for health care workers, who lack appropriate alternatives during the COVID-19 crisis in the spring of 2020. The design (referred to as Pneumask) consists of a custom snorkel-specific adapter that couples the snorkel-port of the mask to a rated filter (either a medical-grade ventilator inline filter or an industrial filter). This design has been tested for the sealing capability of the mask, filter performance, CO2 buildup and clinical usability. These tests found the Pneumask capable of forming a seal that exceeds the standards required for half-face respirators or N95 respirators. Filter testing indicates a range of options with varying performance depending on the quality of filter selected, but with typical filter performance exceeding or comparable to the N95 standard. CO2 buildup was found to be roughly equivalent to levels found in half-face elastomeric respirators in literature. Clinical usability tests indicate sufficient visibility and, while speaking is somewhat muffled, this can be addressed via amplification (Bluetooth voice relay to cell phone speakers through an app) in noisy environments. We present guidance on the assembly, usage (donning and doffing) and decontamination protocols. The benefit of the Pneumask as PPE is that it is reusable for longer periods than typical disposable N95 respirators, as the snorkel mask can withstand rigorous decontamination protocols (that are standard to regular elastomeric respirators). With the dire worldwide shortage of PPE for medical personnel, our conclusions on the performance and efficacy of Pneumask as an N95-alternative technology are cautiously optimistic.

  View details for DOI 10.1371/journal.pone.0244422

  View details for PubMedID 33439902

• Applying heat and humidity using stove boiled water for decontamination of N95 respirators in low resource settings. PloS one Doshi, S., Banavar, S. P., Flaum, E., Kulkarni, S., Vaidya, U., Kumar, S., Chen, T., Bhattacharya, A., Prakash, M. 2021; 16 (9): e0255338

  Abstract

  Global shortages of N95 respirators have led to an urgent need of N95 decontamination and reuse methods that are scientifically validated and available world-wide. Although several large scale decontamination methods have been proposed (hydrogen peroxide vapor, UV-C); many of them are not applicable in remote and low-resource settings. Heat with humidity has been demonstrated as a promising decontamination approach, but care must be taken when implementing this method at a grassroots level. Here we present a simple, scalable method to provide controlled humidity and temperature for individual N95 respirators which is easily applicable in low-resource settings. N95 respirators were subjected to moist heat (>50% relative humidity, 65-80°C temperature) for over 30 minutes by placing them in a sealed container immersed in water that had been brought to a rolling boil and removed from heat, and then allowing the containers to sit for over 45 minutes. Filtration efficiency of 0.3-4.99 μm incense particles remained above 97% after 5 treatment cycles across all particle size sub-ranges. This method was then repeated at a higher ambient temperature and humidity in Mumbai, using standard utensils commonly found in South Asia. Similar temperature and humidity profiles were achieved with no degradation in filtration efficiencies after 6 cycles. Higher temperatures (>70°C) and longer treatment times (>40 minutes) were obtained by insulating the outer vessel. We also showed that the same method can be applied for the decontamination of surgical masks. This simple yet reliable method can be performed even without electricity access using any heat source to boil water, from open-flame stoves to solar heating, and provides a low-cost route for N95 decontamination globally applicable in resource-constrained settings.

  View details for DOI 10.1371/journal.pone.0255338

  View details for PubMedID 34591858

• Sensory Discrimination of Blood and Floral Nectar by Aedes aegypti Mosquitoes. Neuron Jove, V., Gong, Z., Hol, F. J., Zhao, Z., Sorrells, T. R., Carroll, T. S., Prakash, M., McBride, C. S., Vosshall, L. B. 2020

  Abstract

  Blood-feeding mosquitoes survive by feeding on nectar for metabolic energy but require a blood meal to develop eggs. Aedes aegypti females must accurately discriminate blood and nectar because each meal promotes mutually exclusive feeding programs with distinct sensory appendages, meal sizes, digestive tract targets, and metabolic fates. We investigated the syringe-like blood-feeding appendage, the stylet, and discovered that sexually dimorphic stylet neurons taste blood. Using pan-neuronal calcium imaging, we found that blood is detected by four functionally distinct stylet neuron classes, each tuned to specific blood components associated with diverse taste qualities. Stylet neurons are insensitive to nectar-specific sugars and respond to glucose only in the presence of additional blood components. The distinction between blood and nectar is therefore encoded in specialized neurons at the very first level of sensory detection in mosquitoes. This innate ability to recognize blood is the basis of vector-borne disease transmission to millions of people worldwide.

  View details for DOI 10.1016/j.neuron.2020.09.019

  View details for PubMedID 33049200

• BiteOscope, an open platform to study mosquito biting behavior. eLife Hol, F. J., Lambrechts, L., Prakash, M. 2020; 9

  Abstract

  Female mosquitoes need a blood meal to reproduce, and in obtaining this essential nutrient they transmit deadly pathogens. Although crucial for the spread of mosquito-borne diseases, blood feeding remains poorly understood due to technological limitations. Indeed, studies often expose human subjects to assess biting behavior. Here, we present the biteOscope, a device that attracts mosquitoes to a host mimic which they bite to obtain an artificial blood meal. The host mimic is transparent, allowing high-resolution imaging of the feeding mosquito. Using machine learning we extract detailed behavioral statistics describing the locomotion, pose, biting, and feeding dynamics of Aedes aegypti, Aedes albopictus, Anopheles stephensi, and Anopheles coluzzii. In addition to characterizing behavioral patterns, we discover that the common insect repellent DEET repels Anopheles coluzzii upon contact with their legs. The biteOscope provides a new perspective on mosquito blood feeding, enabling the high-throughput quantitative characterization of this lethal behavior.

  View details for DOI 10.7554/eLife.56829

  View details for PubMedID 32960173

• Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays. Nature physics Juan, G. R., Mathijssen, A. J., He, M., Jan, L., Marshall, W., Prakash, M. 2020; 16 (9): 958-964

  Abstract

  Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults [1]. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility [2, 3]. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium [4, 5], collectively moving metachronal waves [6-10], and more generally the hydrodynamics of active matter [11, 12]. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from the sub-cellular (nm) to the organ scales (mm), characterising quantitatively its ciliary arrangement and the generated flows. Locally we measure heterogeneity in both cilia organisation and flow structure, but across the trachea fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of 'stochastic resonance' [13-15], in the sense that noise can improve the function of the system. Taken together, our results shed light on how the microstructure of an active carpet [16, 17] determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies [1], which are the third leading cause of deaths worldwide [18].

  View details for DOI 10.1038/s41567-020-0923-8

  View details for PubMedID 35937969

  View details for PubMedCentralID PMC9355487

• Scale-free vertical tracking microscopy. Nature methods Krishnamurthy, D., Li, H., Benoit du Rey, F., Cambournac, P., Larson, A. G., Li, E., Prakash, M. 2020

  Abstract

  The behavior and microscale processes associated with freely suspended organisms, along with sinking particles underlie key ecological processes in the ocean. Mechanistically studying such multiscale processes in the laboratory presents a considerable challenge for microscopy: how to measure single cells at microscale resolution, while allowing them to freely move hundreds of meters in the vertical direction? Here we present a solution in the form of a scale-free, vertical tracking microscope, based on a 'hydrodynamic treadmill' with no bounds for motion along the axis of gravity. Using this method to bridge spatial scales, we assembled a multiscale behavioral dataset of nonadherent planktonic cells and organisms. Furthermore, we demonstrate a 'virtual-reality system for single cells', wherein cell behavior directly controls its ambient environmental parameters, enabling quantitative behavioral assays. Our method and results exemplify a new paradigm of multiscale measurement, wherein one can observe and probe macroscale and ecologically relevant phenomena at microscale resolution. Beyond the marine context, we foresee that our method will allow biological measurements of cells and organisms in a suspended state by freeing them from the confines of the coverslip.

  View details for DOI 10.1038/s41592-020-0924-7

  View details for PubMedID 32807956

• Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays NATURE PHYSICS Ramirez-San Juan, G. R., Mathijssen, A. M., He, M., Jan, L., Marshall, W., Prakash, M. 2020

  View details for DOI 10.1038/s41567-020-0923-8

  View details for Web of Science ID 000538974700002

• The multiscale physics of cilia and flagella Nature Physics Review Gilpin, W., Bull, M. S., Prakash, M. 2020; 2: 74–88

  View details for DOI 10.1038/s42254-019-0129-0

• An investigation of Dirofilaria immitis infection and its effects on mosquito wingbeat frequencies. Veterinary parasitology Park, D. n., Bowles, J. n., McKenzie, B. n., Narayanan, H. V., Prakash, M. n., Blagburn, B. n., Starkey, L. n., Zohdy, S. n. 2020; 283: 109112

  Abstract

  Each mosquito species has a different wingbeat frequency by which they attract mates. With just a brief recording (<1/10th of a second) these acoustic signatures can be analyzed to quickly determine if mosquitoes belong to a species that is known to transmit different pathogens. A recent study has shown that mobile phones are capable of capturing acoustic data from mosquito wingbeats. We examined wingbeat signatures and flight duration patterns of D. immitis infected and non-infected Aedes aegypti to determine if mobile phone recordings of wingbeat frequencies can be used to distinguish infected mosquitoes from non-infected ones. Female mosquitoes were recorded prior to and at various time points after feeding on infected or non-infected dog blood by placing individual mosquitoes into a collection vial and recording for 60 s using the Voice Memo app for iPhone 7 plus and 8. To uniformly analyze audio data, recordings were processed using a previously described automated algorithm in Python 3.0 to determine wingbeat frequency. A total of 1669 recordings were gathered, and mosquitoes were dissected to confirm the presence and number of D. immitis larvae. Our findings indicate that there was a significant effect on wingbeat frequency with an increasing number of L3 larvae. Specifically, as the number of L3, infective stage larvae increases, a decrease in wingbeat frequency is seen. However, there was no significant effect of increasing number of L1 or L2 larvae causing increasing wingbeat frequencies. The detection of a significant difference in wingbeat frequencies between mosquitoes harboring infective stage D. immitis larvae is unique and suggests the possibility of using wingbeat recordings as a tool for vector species and pathogen surveillance and monitoring.

  View details for DOI 10.1016/j.vetpar.2020.109112

  View details for PubMedID 32512421

• Coupled Active Systems Encode an Emergent Hunting Behavior in the Unicellular Predator Lacrymaria olor. Current biology : CB Coyle, S. M., Flaum, E. M., Li, H., Krishnamurthy, D., Prakash, M. 2019

  Abstract

  Many single-celled protists use rapid morphology changes to perform fast animal-like behaviors. To understand how such behaviors are encoded, we analyzed the hunting dynamics of the predatory ciliate Lacrymaria olor, which locates and captures prey using the tip of a slender "neck" that can rapidly extend more than seven times its body length (500mum from its body) and retract in seconds. By tracking single cells in real-time over hours and analyzing millions of sub-cellular postures, we find that these fast extension-contraction cycles underlie an emergent hunting behavior that comprehensively samples a broad area within the cell's reach. Although this behavior appears complex, we show that it arises naturally as alternating sub-cellular ciliary and contractile activities rearrange the cell's underlying helical cytoskeleton to extend or retract the neck. At short timescales, a retracting neck behaves like an elastic filament under load, such that compression activates a series of buckling modes that reorient the head and scramble its extensile trajectory. At longer timescales, the fundamental length of this filament can change, altering the location in space where these transitions occur. Coupling these fast and slow dynamics together, we present a simple model for how Lacrymaria samples the range of geometries and orientations needed to ensure dense stochastic sampling of the immediate environment when hunting to locate and strike at prey. More generally, coupling active mechanical and chemical signaling systems across different timescales may provide a general strategy by which mechanically encoded emergent cell behaviors can be understood or engineered.

  View details for DOI 10.1016/j.cub.2019.09.034

  View details for PubMedID 31679941

• Collective intercellular communication through ultra-fast hydrodynamic trigger waves. Nature Mathijssen, A. J., Culver, J., Bhamla, M. S., Prakash, M. 2019

  Abstract

  The biophysical relationships between sensors and actuators1-5 have been fundamental to the development of complex life forms. Swimming organisms generate abundant flows that persist in aquatic environments6-13, and responding promptly to external stimuli is key to survival14-19. Here we present the discovery of 'hydrodynamic trigger waves' in cellular communities of the protist Spirostomum ambiguum that propagate-in a manner similar to a chain reaction20-22-hundreds of times faster than their swimming speed. By coiling its cytoskeleton, Spirostomum can contract its long body by 60% within milliseconds23, experiencing accelerations that can reach forces of 14g. We show that a single cellular contraction (the transmitter) generates long-ranged vortex flows at intermediate Reynolds numbers that can, in turn, trigger neighbouring cells (the receivers). To measure the sensitivity to hydrodynamic signals in these receiver cells, we present a high-throughput suction-flow device for probing mechanosensitive ion channels24 by back-calculating the microscopic forces on the cell membrane. We analyse and quantitatively model the ultra-fast hydrodynamic trigger waves in a universal framework of antenna and percolation theory25,26, and reveal a phase transition that requires a critical colony density to sustain collective communication. Our results suggest that this signalling could help to organize cohabiting communities over large distances and influence long-term behaviour through gene expression (comparable to quorum sensing16). In more immediate terms, because contractions release toxins27, synchronized discharges could facilitate the repulsion of large predators or immobilize large prey. We postulate that numerous aquatic organisms other than protists could coordinate their behaviour using variations of hydrodynamic trigger waves.

  View details for DOI 10.1038/s41586-019-1387-9

  View details for PubMedID 31292551

• BITES, BLOOD AND BEHAVIOR: BIOPHYSICAL APPROACHES TO UNDERSTANDING MOSQUITO BLOOD-FEEDING BEHAVIOR Hol, F. J., Lambrechts, L., Prakash, M. AMER SOC TROP MED & HYGIENE. 2019: 444

  View details for Web of Science ID 000507364504156

• Frugal Science in the Age of Curiosity Manu Prakash, Jim Cybulski, Rebecca Konte, Team Foldscope and the global Foldscope community Prakash, M., Cybulski, J., Konte, R., Team Foldscope Global Foldscope Co edited by Boucher, M. P., Helmreich, S., Kinney, L. W., Tibbits, S., Uchill, R., Ziporyn, E. MIT PRESS. 2019: 26–29

  View details for Web of Science ID 000546472600005

• VECTOR CHIP: A MINIATURIZED PLATFORM FOR HIGH-THROUGHPUT INTERROGATION OF MOSQUITO-PATHOGEN DYNAMICS Kumar, S., Hol, F., Prakash, M. AMER SOC TROP MED & HYGIENE. 2019: 421–22

  View details for Web of Science ID 000507364504082

• OPENMM - A LOW-COST, MODULAR, AND AUTONOMOUS MICROSCOPE FOR MALARIA DIAGNOSIS AND BEYOND Li, H., Soto-Montoya, H., Valenzuela, L. F., Voisin, M., Prakash, M. AMER SOC TROP MED & HYGIENE. 2019: 484

  View details for Web of Science ID 000507364504290

• ABUZZ : A MOBILE PHONE BASED CITIZEN SCIENCE PLATFORM FOR CROWDSOURCING ECOLOGICAL DATA FOR MOSQUITO SURVEILLANCE Mukundarajan, H., Konte, R., Hol, F. J., Soto-Montoya, H., Murphy, A., McKenzie, B., Abernethy, S., Park, D., Zohdy, S., Prakash, M. AMER SOC TROP MED & HYGIENE. 2019: 448

  View details for Web of Science ID 000507364504170

• Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity. Proceedings of the National Academy of Sciences of the United States of America Armon, S., Bull, M. S., Aranda-Diaz, A., Prakash, M. 2018

  Abstract

  By definition of multicellularity, all animals need to keep their cells attached and intact, despite internal and external forces. Cohesion between epithelial cells provides this key feature. To better understand fundamental limits of this cohesion, we study the epithelium mechanics of an ultrathin (25 mum) primitive marine animal Trichoplax adhaerens, composed essentially of two flat epithelial layers. With no known extracellular matrix and no nerves or muscles, T. adhaerens has been claimed to be the "simplest known living animal," yet is still capable of coordinated locomotion and behavior. Here we report the discovery of the fastest epithelial cellular contractions known in any metazoan, to be found in T. adhaerens dorsal epithelium (50% shrinkage of apical cell area within one second, at least an order of magnitude faster than other known examples). Live imaging reveals emergent contractile patterns that are mostly sporadic single-cell events, but also include propagating contraction waves across the tissue. We show that cell contraction speed can be explained by current models of nonmuscle actin-myosin bundles without load, while the tissue architecture and unique mechanical properties are softening the tissue, minimizing the load on a contracting cell. We propose a hypothesis, in which the physiological role of the contraction dynamics is to resist external stresses while avoiding tissue rupture ("active cohesion"), a concept that can be further applied to engineering of active materials.

  View details for PubMedID 30309963

• Two-component marangoni-contracted droplets: friction and shape SOFT MATTER Benusiglio, A., Cira, N. J., Prakash, M. 2018; 14 (37): 7724–30

  View details for DOI 10.1039/c7sm02361h

  View details for Web of Science ID 000448354800018

• Two-component marangoni-contracted droplets: friction and shape. Soft matter Benusiglio, A., Cira, N. J., Prakash, M. 2018

  Abstract

  When a mixture of propylene glycol and water is deposited on a clean glass slide, it forms a droplet of a given apparent contact angle rather than spreading as one would expect on such a high-energy surface. The droplet is stabilized by a Marangoni flow due to the non-uniformity of the components' concentrations between the border and the apex of the droplet, itself a result of evaporation. These self-contracting droplets have unusual properties such as absence of pinning and the ability to move under an external humidity gradient. The droplets' apparent contact angles are a function of their concentration and the external humidity. Here we study the motion of such droplets sliding down slopes and compare the results to normal non-volatile droplets. We precisely control the external humidity and explore the influence of the volume, viscosity, surface tension, and contact angle. We find that the droplets suffer a negligible pinning force so that for small velocities the capillary number (Ca) is directly proportional to the Bond number (Bo): Ca = Bosinalpha with alpha the angle of the slope. Lastly we study the successive shapes the droplets take when sliding at larger and larger velocities.

  View details for PubMedID 30191241

• The principles of cascading power limits in small, fast biological and engineered systems SCIENCE Ilton, M., Bhamla, M., Ma, X., Cox, S. M., Fitchett, L. L., Kim, Y., Koh, J., Krishnamurthy, D., Kuo, C., Temel, F., Crosby, A. J., Prakash, M., Sutton, G. P., Wood, R. J., Azizi, E., Bergbreiter, S., Patek, S. N. 2018; 360 (6387): 397-+

  Abstract

  Mechanical power limitations emerge from the physical trade-off between force and velocity. Many biological systems incorporate power-enhancing mechanisms enabling extraordinary accelerations at small sizes. We establish how power enhancement emerges through the dynamic coupling of motors, springs, and latches and reveal how each displays its own force-velocity behavior. We mathematically demonstrate a tunable performance space for spring-actuated movement that is applicable to biological and synthetic systems. Incorporating nonideal spring behavior and parameterizing latch dynamics allows the identification of critical transitions in mass and trade-offs in spring scaling, both of which offer explanations for long-observed scaling patterns in biological systems. This analysis defines the cascading challenges of power enhancement, explores their emergent effects in biological and engineered systems, and charts a pathway for higher-level analysis and synthesis of power-amplified systems.

  View details for PubMedID 29700237

• Synchronous magnetic control of water droplets in bulk ferrofluid SOFT MATTER Katsikis, G., Breant, A., Rinberg, A., Prakash, M. 2018; 14 (5): 681–92

  Abstract

  We present a microfluidic platform for magnetic manipulation of water droplets immersed in bulk oil-based ferrofluid. Although non-magnetic, the droplets are exclusively controlled by magnetic fields without any pressure-driven flow. The fluids are dispensed in a sub-millimeter Hele-Shaw chamber that includes permalloy tracks on its substrate. An in-plane rotating magnetic field magnetizes the permalloy tracks, producing local magnetic gradients, while an orthogonal magnetic field magnetizes the bulk ferrofluid. To minimize the magnetostatic energy of the system, the water droplets are attracted towards the locations on the tracks where the bulk ferrofluid is repelled. Using this technique, we demonstrate synchronous generation and propagation of water droplets, study the kinematics of propagation, and analyze the flow of the bulk ferrofluid. In addition, we show controlled break-up of droplets and droplet-to-droplet interactions. Finally, we discuss future applications owing to the potential biocompatibility of the droplets.

  View details for PubMedID 29205244

• Ultra Fast Contractions and Emergent Dynamics in a Living Active Solid - The Epithelium of the Primitive Animal Trichoplax adhaerens Armon, S., Prakash, M. CELL PRESS. 2018: 649A

  View details for Web of Science ID 000430563300236

• Local Epithelial Fracture and Healing Mechanics Dictate Morphogenesis and Asexual Reproduction in Trichoplax adhaerens Prakash, V. N., Bhargava, A., Prakash, M. CELL PRESS. 2018: 651A–652A

  View details for Web of Science ID 000430563300252

• Using mobile phones as acoustic sensors for high-throughput mosquito surveillance ELIFE Mukundarajan, H., Hol, F., Castillo, E., Newby, C., Prakash, M. 2017; 6

  Abstract

  The direct monitoring of mosquito populations in field settings is a crucial input for shaping appropriate and timely control measures for mosquito-borne diseases. Here, we demonstrate that commercially available mobile phones are a powerful tool for acoustically mapping mosquito species distributions worldwide. We show that even low-cost mobile phones with very basic functionality are capable of sensitively acquiring acoustic data on species-specific mosquito wingbeat sounds, while simultaneously recording the time and location of the human-mosquito encounter. We survey a wide range of medically important mosquito species, to quantitatively demonstrate how acoustic recordings supported by spatio-temporal metadata enable rapid, non-invasive species identification. As proof-of-concept, we carry out field demonstrations where minimally-trained users map local mosquitoes using their personal phones. Thus, we establish a new paradigm for mosquito surveillance that takes advantage of the existing global mobile network infrastructure, to enable continuous and large-scale data acquisition in resource-constrained areas.

  View details for PubMedID 29087296

• Flowtrace: simple visualization of coherent structures in biological fluid flows JOURNAL OF EXPERIMENTAL BIOLOGY Gilpin, W., Prakash, V. N., Prakash, M. 2017; 220 (19): 3411–18

  Abstract

  We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results with more experimentally difficult and mathematically sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential 'middle ground' allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques. In addition to being informative, the visualizations generated by our tool are often striking and elegant, illustrating coherent structures directly from videos without the need for computational overlays. Our tool is available as fully documented open-source code for MATLAB, Python or ImageJ at www.flowtrace.org.

  View details for PubMedID 28729343

• Generation of droplet arrays with rational number spacing patterns driven by a periodic energy landscape PHYSICAL REVIEW E Rinberg, A., Katsikis, G., Prakash, M. 2017; 96 (3): 033108

  Abstract

  The generation of droplets at low Reynolds numbers is driven by nonlinear dynamics that give rise to complex patterns concerning both the droplet-to-droplet spacing and the individual droplet sizes. Here we demonstrate an experimental system in which a time-varying energy landscape provides a periodic magnetic force that generates an array of droplets from an immiscible mixture of ferrofluid and silicone oil. The resulting droplet patterns are periodic, owing to the nature of the magnetic force, yet the droplet spacing and size can vary greatly by tuning a single bias pressure applied on the ferrofluid phase; for a given cycle period of the magnetic force, droplets can be generated either at integer multiples (1, 2, ...), or at rational fractions (3/2, 5/3, 5/2, ...) of this period with mono- or multidisperse droplet sizes. We develop a discrete-time dynamical systems model not only to reproduce the phenotypes of the observed patterns but also to provide a framework for understanding systems driven by such periodic energy landscapes.

  View details for PubMedID 29346989

• Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and Redundancy. Current biology : CB Elting, M. W., Prakash, M., Udy, D. B., Dumont, S. 2017; 27 (14): 2112-2122.e5

  Abstract

  Active forces generated at kinetochores move chromosomes, and the dynamic spindle must robustly anchor kinetochore fibers (k-fibers) to bear this load. The mammalian spindle bears the load of chromosome movement far from poles, but we do not know where and how-physically and molecularly-this load distributes across the spindle. In part, this is because probing spindle mechanics in live cells is difficult. Yet answering this question is key to understanding how the spindle generates and responds to force and performs its diverse mechanical functions. Here, we map load-bearing across the mammalian spindle in space-time and dissect local anchorage mechanics and mechanism. To do so, we laser-ablate single k-fibers at different spindle locations and in different molecular backgrounds and quantify the immediate relaxation of chromosomes, k-fibers, and microtubule speckles. We find that load redistribution is locally confined in all directions: along the first 3-4 μm from kinetochores, scaling with k-fiber length, and laterally within ∼2 μm of k-fiber sides, without detectable load sharing between neighboring k-fibers. A phenomenological model suggests that dense, transient crosslinks to the spindle along k-fibers bear the load of chromosome movement but that these connections do not limit the timescale of spindle reorganization. The microtubule crosslinker NuMA is needed for the local load-bearing observed, whereas Eg5 and PRC1 are not detectably required, suggesting specialization in mechanical function. Together, the data and model suggest that NuMA-mediated crosslinks locally bear load, providing mechanical isolation and redundancy while allowing spindle fluidity. These features are well suited to support robust chromosome segregation.

  View details for DOI 10.1016/j.cub.2017.06.018

  View details for PubMedID 28690110

  View details for PubMedCentralID PMC5579025

• Vortex arrays and ciliary tangles underlie the feeding-swimming trade-off in starfish larvae NATURE PHYSICS Gilpin, W., Prakash, V. N., Prakash, M. 2017; 13 (4): 380-386

  View details for DOI 10.1038/NPHYS3981

  View details for Web of Science ID 000398262900018

• Schistosoma mansoni cercariae swim effciently by exploiting an elastohydrodynamic coupling NATURE PHYSICS Krishnamurthy, D., Katsikis, G., Bhargava, A., Prakash, M. 2017; 13 (3): 266-271

  View details for DOI 10.1038/NPHYS3924

  View details for Web of Science ID 000395814000018

• USING MOBILE PHONES AS ACOUSTIC SENSORS FOR HIGH-THROUGHPUT SURVEILLANCE OF MOSQUITO ECOLOGY Mukundarajan, H., Hol, F., Castillo, E., Newby, C., Prakash, M. AMER SOC TROP MED & HYGIENE. 2017: 21

  View details for Web of Science ID 000423215202065

• Hand-powered ultralow-cost paper centrifuge NATURE BIOMEDICAL ENGINEERING Bhamla, M., Benson, B., Chai, C., Katsikis, G., Johri, A., Prakash, M. 2017; 1 (1)

  View details for DOI 10.1038/s41551-016-0009

  View details for Web of Science ID 000418850600009

• Wetting: Bumps lead the way. Nature materials Prakash, M. 2016; 15 (4): 378-379

  View details for DOI 10.1038/nmat4612

  View details for PubMedID 27005915

• Surface tension dominates insect flight on fluid interfaces. journal of experimental biology Mukundarajan, H., Bardon, T. C., Kim, D. H., Prakash, M. 2016; 219: 752-766

  Abstract

  Flight on the 2D air-water interface, with body weight supported by surface tension, is a unique locomotion strategy well adapted for the environmental niche on the surface of water. Although previously described in aquatic insects like stoneflies, the biomechanics of interfacial flight has never been analysed. Here, we report interfacial flight as an adapted behaviour in waterlily beetles (Galerucella nymphaeae) which are also dexterous airborne fliers. We present the first quantitative biomechanical model of interfacial flight in insects, uncovering an intricate interplay of capillary, aerodynamic and neuromuscular forces. We show that waterlily beetles use their tarsal claws to attach themselves to the interface, via a fluid contact line pinned at the claw. We investigate the kinematics of interfacial flight trajectories using high-speed imaging and construct a mathematical model describing the flight dynamics. Our results show that non-linear surface tension forces make interfacial flight energetically expensive compared with airborne flight at the relatively high speeds characteristic of waterlily beetles, and cause chaotic dynamics to arise naturally in these regimes. We identify the crucial roles of capillary-gravity wave drag and oscillatory surface tension forces which dominate interfacial flight, showing that the air-water interface presents a radically modified force landscape for flapping wing flight compared with air.

  View details for DOI 10.1242/jeb.127829

  View details for PubMedID 26936640

  View details for PubMedCentralID PMC4811005

• Synchronous universal droplet logic and control NATURE PHYSICS Katsikis, G., Cybulski, J. S., Prakash, M. 2015; 11 (7): 588-596

  View details for DOI 10.1038/NPHYS3341

  View details for Web of Science ID 000357197300026

• Diagnosis of Schistosoma haematobium Infection with a Mobile Phone-Mounted Foldscope and a Reversed-Lens CellScope in Ghana AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Ephraim, R. K., Duah, E., Cybulski, J. S., Prakash, M., D'Ambrosio, M. V., Fletcher, D. A., Keiser, J., Andrews, J. R., Bogoch, I. I. 2015; 92 (6): 1253-1256

  Abstract

  We evaluated two novel, portable microscopes and locally acquired, single-ply, paper towels as filter paper for the diagnosis of Schistosoma haematobium infection. The mobile phone-mounted Foldscope and reversed-lens CellScope had sensitivities of 55.9% and 67.6%, and specificities of 93.3% and 100.0%, respectively, compared with conventional light microscopy for diagnosing S. haematobium infection. With conventional light microscopy, urine filtration using single-ply paper towels as filter paper showed a sensitivity of 67.6% and specificity of 80.0% compared with centrifugation for the diagnosis of S. haematobium infection. With future improvements to diagnostic sensitivity, newer generation handheld and mobile phone microscopes may be valuable tools for global health applications.

  View details for DOI 10.4269/ajtmh.14-0741

  View details for Web of Science ID 000355785400028

  View details for PubMedID 25918211

• Vapour-mediated sensing and motility in two-component droplets. Nature Cira, N. J., Benusiglio, A., PRAKASH, M. 2015; 519 (7544): 446-450

  Abstract

  Controlling the wetting behaviour of liquids on surfaces is important for a variety of industrial applications such as water-repellent coatings and lubrication. Liquid behaviour on a surface can range from complete spreading, as in the 'tears of wine' effect, to minimal wetting as observed on a superhydrophobic lotus leaf. Controlling droplet movement is important in microfluidic liquid handling, on self-cleaning surfaces and in heat transfer. Droplet motion can be achieved by gradients of surface energy. However, existing techniques require either a large gradient or a carefully prepared surface to overcome the effects of contact line pinning, which usually limit droplet motion. Here we show that two-component droplets of well-chosen miscible liquids such as propylene glycol and water deposited on clean glass are not subject to pinning and cause the motion of neighbouring droplets over a distance. Unlike the canonical predictions for these liquids on a high-energy surface, these droplets do not spread completely but exhibit an apparent contact angle. We demonstrate experimentally and analytically that these droplets are stabilized by evaporation-induced surface tension gradients and that they move in response to the vapour emitted by neighbouring droplets. Our fundamental understanding of this robust system enabled us to construct a wide variety of autonomous fluidic machines out of everyday materials.

  View details for DOI 10.1038/nature14272

  View details for PubMedID 25762146

• Vapour-mediated sensing and motility in two-component droplets NATURE Cira, N. J., Benusiglio, A., Prakash, M. 2015; 519 (7544): 446-?

  View details for DOI 10.1038/nature14272

  View details for Web of Science ID 000351602800051

  View details for PubMedID 25762146

• Punch card programmable microfluidics. PloS one Korir, G., Prakash, M. 2015; 10 (3)

  Abstract

  Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.

  View details for DOI 10.1371/journal.pone.0115993

  View details for PubMedID 25738834

  View details for PubMedCentralID PMC4349784

• Punch card programmable microfluidics. PloS one Korir, G., Prakash, M. 2015; 10 (3): e0115993

  Abstract

  Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.

  View details for DOI 10.1371/journal.pone.0115993

  View details for PubMedID 25738834

  View details for PubMedCentralID PMC4349784

• Emergent mechanics of biological structures MOLECULAR BIOLOGY OF THE CELL Dumont, S., Prakash, M. 2014; 25 (22): 3461-3465

  View details for DOI 10.1091/mbc.E14-03-0784

  View details for Web of Science ID 000344236800007

• Emergent mechanics of biological structures. Molecular biology of the cell Dumont, S., Prakash, M. 2014; 25 (22): 3461-3465

  Abstract

  Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework "emergent mechanics." Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead.

  View details for DOI 10.1091/mbc.E14-03-0784

  View details for PubMedID 25368421

  View details for PubMedCentralID PMC4230603

• Foldscope: Origami-Based Paper Microscope PLOS ONE Cybulski, J. S., Clements, J., Prakash, M. 2014; 9 (6)

  Abstract

  Here we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.

  View details for DOI 10.1371/journal.pone.0098781

  View details for Web of Science ID 000338508200010

  View details for PubMedCentralID PMC4062392

• Probing the Mechanical Coupling of the Cell Membrane to the Nucleus with Vertical Nanopillar Arrays 57th Annual Meeting of the Biophysical-Society Hanson, L., Urzay, J., Lin, Z., Zhao, W., Prakash, M., Cui, B. CELL PRESS. 2013: 546A–546A

  View details for Web of Science ID 000316074305286

• Hydraulic stress induced bubble nucleation and growth during pupal metamorphosis Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB)/Symposium on New Frontiers from Marine Snakes to Marine Ecosystems Prakash, M. OXFORD UNIV PRESS INC. 2012: E140–E140

  View details for Web of Science ID 000303165001028

• Flying in two dimensions Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB)/Symposium on New Frontiers from Marine Snakes to Marine Ecosystems Prakash, M., Donald, K. OXFORD UNIV PRESS INC. 2012: E141–E141

  View details for Web of Science ID 000303165001029

• The hungry fly: Hydrodynamics of feeding in the common house fly PHYSICS OF FLUIDS Prakash, M., Steele, M. 2011; 23 (9)

  View details for DOI 10.1063/1.3640023

  View details for Web of Science ID 000295621800010

• Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis NATURE MATERIALS Joo, J., Chow, B. Y., Prakash, M., Boyden, E. S., Jacobson, J. M. 2011; 10 (8): 596-601

  Abstract

  Rational control over the morphology and the functional properties of inorganic nanostructures has been a long-standing goal in the development of bottom-up device fabrication processes. We report that the geometry of hydrothermally grown zinc oxide nanowires can be tuned from platelets to needles, covering more than three orders of magnitude in aspect ratio (~0.1-100). We introduce a classical thermodynamics-based model to explain the underlying growth inhibition mechanism by means of the competitive and face-selective electrostatic adsorption of non-zinc complex ions at alkaline conditions. The performance of these nanowires rivals that of vapour-phase-grown nanostructures, and their low-temperature synthesis (<60 °C) is favourable to the integration and in situ fabrication of complex and polymer-supported devices. We illustrate this capability by fabricating an all-inorganic light-emitting diode in a polymeric microfluidic manifold. Our findings indicate that electrostatic interactions in aqueous crystal growth may be systematically manipulated to synthesize nanostructures and devices with enhanced structural control.

  View details for DOI 10.1038/NMAT3069

  View details for Web of Science ID 000293000000019

  View details for PubMedID 21743451

• Hydraulic stress induced bubble nucleation and growth during pupal metamorphosis Annual Meeting of the American-Society-for-Cell-Biology (ASCB) PRAKASH, M. AMER SOC CELL BIOLOGY. 2011

  View details for Web of Science ID 000305505501236

• Face-selective electrostatic control of nanowire synthesis Nature Materials Joo, J., Chow, B., Prakash, M., Boyden, E., Jacobson, J. 2011; 10: 596-601
• Interfacial Propulsion by Directional Adhesion International Journal of Non-Linear Mechanics Manu Prakash, John W. M. Bush 2011; 46 (4): 607-615
• On a tweezer for droplets Advances in Colloid and Interface Science Bush, J., Peaudecerf, F., Prakash, M., Quere, D. 2010; 161: 10-14
• Drop propulsion in tapered tubes Euro Physics Letters, Renvoise, P., Bush, J., Prakash, M., Quere, D. 2009; 86: 1-5
• Surface tension transport of prey by feeding shorebirds: The capillary ratchet SCIENCE Prakash, M., Quere, D., Bush, J. W. 2008; 320 (5878): 931-934

  Abstract

  The variability of bird beak morphology reflects diverse foraging strategies. One such feeding mechanism in shorebirds involves surface tension-induced transport of prey in millimetric droplets: By repeatedly opening and closing its beak in a tweezering motion, the bird moves the drop from the tip of its beak to its mouth in a stepwise ratcheting fashion. We have analyzed the subtle physical mechanism responsible for drop transport and demonstrated experimentally that the beak geometry and the dynamics of tweezering may be tuned to optimize transport efficiency. We also highlight the critical dependence of the capillary ratchet on the beak's wetting properties, thus making clear the vulnerability of capillary feeders to surface pollutants.

  View details for DOI 10.1126/science.1156023

  View details for Web of Science ID 000255868300042

  View details for PubMedID 18487193

• Microfluidic bubble logic SCIENCE Prakash, M., Gershenfeld, N. 2007; 315 (5813): 832-835

  Abstract

  We demonstrate universal computation in an all-fluidic two-phase microfluidic system. Nonlinearity is introduced into an otherwise linear, reversible, low-Reynolds number flow via bubble-to-bubble hydrodynamic interactions. A bubble traveling in a channel represents a bit, providing us with the capability to simultaneously transport materials and perform logical control operations. We demonstrate bubble logic AND/OR/NOT gates, a toggle flip-flop, a ripple counter, timing restoration, a ring oscillator, and an electro-bubble modulator. These show the nonlinearity, gain, bistability, synchronization, cascadability, feedback, and programmability required for scalable universal computation. With increasing complexity in large-scale microfluidic processors, bubble logic provides an on-chip process control mechanism integrating chemistry and computation.

  View details for DOI 10.1126/science.1136907

  View details for Web of Science ID 000244069000065

  View details for PubMedID 17289994

• The Integument of Water-walking Arthropods: Form and Function Advances in Insect Physiology John W. M. Bush, David L. Hu, Manu Prakash 2007; 34: 117-192
• Water walking devices Experiments in Fluids Hu, D., Prakash, M., Chan, B., Bush, J. 2007; 43: 769-778
• Microfludic Bubble Logic Science Prakash, M., Gershenfeld, N. 2007; 315: 832-835
• Personal fabrication Telektronikk Gershenfeld, N., Prakash, M. 2004; 3: 22-26