Persistence of plasmids targeted by CRISPR interference in bacterial populations.

CRISPR-Cas systems provide prokaryotes with an RNA-guided defense against foreign mobile genetic elements (MGEs) such as plasmids and viruses. A common mechanism by which MGEs avoid interference by CRISPR consists of acquisition of escape mutations in regions targeted by CRISPR. Here, using microbiological, live microscopy and microfluidics analyses we demonstrate that plasmids can persist for multiple generations in some Escherichia coli cell lineages at conditions of continuous targeting by the type I-E CRISPR-Cas system. We used mathematical modeling to show how plasmid persistence in a subpopulation of cells mounting CRISPR interference is achieved due to the stochastic nature of CRISPR interference and plasmid replication events. We hypothesize that the observed complex dynamics provides bacterial populations with long-term benefits due to continuous maintenance of mobile genetic elements in some cells, which leads to diversification of phenotypes in the entire community and allows rapid changes in the population structure to meet the demands of a changing environment.

One-Pot Synthesis of Affordable Redox-Responsive Drug Delivery System Based on Trithiocyanuric Acid Nanoparticles.

Redox-responsive drug delivery systems present a promising avenue for drug delivery due to their ability to leverage the unique redox environment within tumor cells. In this work, we describe a facile and cost-effective one-pot synthesis method for a redox-responsive delivery system based on novel trithiocyanuric acid (TTCA) nanoparticles (NPs). We conduct a thorough investigation of the impact of various synthesis parameters on the morphology, stability, and loading capacity of these NPs. The great drug delivery potential of the system is further demonstrated in vitro and in vivo by using doxorubicin as a model drug. The developed TTCA-PEG NPs show great drug delivery efficiency with minimal toxicity on their own both in vivo and in vitro. The simplicity of this synthesis, along with the promising characteristics of TTCA-PEG NPs, paves the way for new opportunities in the further development of redox-responsive drug delivery systems based on TTCA.

Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore.

Currently, nanopore-based technology for the determination of the functional activity of single enzyme molecules continues its development. The use of natural nanopores for studying single enzyme molecules is known. At that, the approach utilizing artificial solid-state nanopores is also promising but still understudied. Herein, we demonstrate the use of a nanotechnology-based approach for the investigation of the enzymatic activity of a single molecule of horseradish peroxidase with a solid-state nanopore. The artificial 5 nm solid-state nanopore has been formed in a 40 nm thick silicon nitride structure. A single molecule of HRP has been entrapped into the nanopore. The activity of the horseradish peroxidase (HRP) enzyme molecule inserted in the nanopore has been monitored by recording the time dependence of the ion current through the nanopore in the course of the reaction of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) oxidation reaction. We have found that in the process of ABTS oxidation in the presence of 2.5 mM hydrogen peroxide, individual HRP enzyme molecules are able to retain activity for approximately 700 s before a decrease in the ion current through the nanopore, which can be explained by structural changes of the enzyme.

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity.

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity.

Bimodal rheotactic behavior reflects flagellar beat asymmetry in human sperm cells.

Rheotaxis, the directed response to fluid velocity gradients, has been shown to facilitate stable upstream swimming of mammalian sperm cells along solid surfaces, suggesting a robust physical mechanism for long-distance navigation during fertilization. However, the dynamics by which a human sperm orients itself relative to an ambient flow is poorly understood. Here, we combine microfluidic experiments with mathematical modeling and 3D flagellar beat reconstruction to quantify the response of individual sperm cells in time-varying flow fields. Single-cell tracking reveals two kinematically distinct swimming states that entail opposite turning behaviors under flow reversal. We constrain an effective 2D model for the turning dynamics through systematic large-scale parameter scans, and find good quantitative agreement with experiments at different shear rates and viscosities. Using a 3D reconstruction algorithm to identify the flagellar beat patterns causing left or right turning, we present comprehensive 3D data demonstrating the rolling dynamics of freely swimming sperm cells around their longitudinal axis. Contrary to current beliefs, this 3D analysis uncovers ambidextrous flagellar waveforms and shows that the cell's turning direction is not defined by the rolling direction. Instead, the different rheotactic turning behaviors are linked to a broken mirror symmetry in the midpiece section, likely arising from a buckling instability. These results challenge current theoretical models of sperm locomotion.

Anticancer Drugs Paclitaxel, Carboplatin, Doxorubicin, and Cyclophosphamide Alter the Biophysical Characteristics of Red Blood Cells, In Vitro.

Red blood cells (RBCs) are the most numerous cells in the body and perform gas exchange between all tissues. During the infusion of cancer chemotherapeutic (CT) agents, blood cells are the first ones to encounter aggressive cytostatics. Erythrocyte dysfunction caused by direct cytotoxic damage might be a part of the problem of chemotherapy-induced anemia-one of the most frequent side effects. The aim of the current study is to evaluate the functional status of RBCs exposed to mono and combinations of widely used commercial pharmaceutical CT drugs with different action mechanisms: paclitaxel, carboplatin, cyclophosphamide, and doxorubicin, in vitro. Using laser diffraction, flow cytometry, and confocal microscopy, we show that paclitaxel, having a directed effect on cytoskeleton proteins, by itself and in combination with carboplatin, caused the most marked abnormalities-loss of control of volume regulation, resistance to osmotic load, and stomatocytosis. Direct simulations of RBCs' microcirculation in microfluidic channels showed both the appearance of a subpopulation of cells with impaired velocity (slow damaged cells) and an increased number of cases of occlusions. In contrast to paclitaxel, such drugs as carboplatin, cyclophosphamide, and doxorubicin, whose main target in cancer cells is DNA, showed significantly less cytotoxicity to erythrocytes in short-term exposure. However, the combination of drugs had an additive effect. While the obtained results should be confirmed in in vivo models, one can envisioned that such data could be used for minimizing anemia side effects during cancer chemotherapy.

Drug-Eluting Sandwich Hydrogel Lenses Based on Microchamber Film Drug Encapsulation.

Corticosteroids are widely used as an anti-inflammatory treatment for eye inflammation, but the current methods used in clinical practice for delivery are in the form of eye drops which is usually complicated for patients or ineffective. This results in an increase in the risk of detrimental side effects. In this study, we demonstrated proof-of-concept research for the development of a contact lens-based delivery system. The sandwich hydrogel contact lens consists of a polymer microchamber film made via soft lithography with an encapsulated corticosteroid, in this case, dexamethasone, located inside the contact lens. The developed delivery system showed sustained and controlled release of the drug. The central visual part of the lenses was cleared from the polylactic acid microchamber in order to maintain a clean central aperture similar to the cosmetic-colored hydrogel contact lenses.

Microfluidic Bi-Layer Platform to Study Functional Interaction between Co-Cultured Neural Networks with Unidirectional Synaptic Connectivity.

The complex synaptic connectivity architecture of neuronal networks underlies cognition and brain function. However, studying the spiking activity propagation and processing in heterogeneous networks in vivo poses significant challenges. In this study, we present a novel two-layer PDMS chip that facilitates the culturing and examination of the functional interaction of two interconnected neural networks. We utilized cultures of hippocampal neurons grown in a two-chamber microfluidic chip combined with a microelectrode array. The asymmetric configuration of the microchannels between the chambers ensured the growth of axons predominantly in one direction from the Source chamber to the Target chamber, forming two neuronal networks with unidirectional synaptic connectivity. We showed that the local application of tetrodotoxin (TTX) to the Source network did not alter the spiking rate in the Target network. The results indicate that stable network activity in the Target network was maintained for at least 1-3 h after TTX application, demonstrating the feasibility of local chemical activity modulation and the influence of electrical activity from one network on the other. Additionally, suppression of synaptic activity in the Source network by the application of CPP and CNQX reorganized spatio-temporal characteristics of spontaneous and stimulus-evoked spiking activity in the Target network. The proposed methodology and results provide a more in-depth examination of the network-level functional interaction between neural circuits with heterogeneous synaptic connectivity.

Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples.

Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX. Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients' blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses. Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression. Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes.

Printed asymmetric microcapsules: Facile loading and multiple stimuli-responsiveness.

Engineering of colloidal particles and capsules despite substantial progress is still facing a number of unsolved issues including low loading capacity, non-uniform size and shape of carriers, tailoring different functionalities and versatility to encapsulated cargo. In this work, we propose a method for defined-shaped functionally asymmetric polymer capsule fabrication based on a soft lithography approach. The developed capsules consist of two classes of polymers - the main part "cup" is made out of polyelectrolyte multilayers (PAH-PSS) and "lid" is made of biodegradable polyether (PLGA). Asymmetric capsules combine advantages from both traditional layer-by-layer capsules and recently developed printed "pelmeni" capsules. This combination provides stimuli-responsiveness due to polyelectrolyte multilayer properties differing from PLGA. The inner volume of capsules can be loaded with a variety of active compounds and the capsule's geometry is defined due to the soft-lithography method. Capsules have a core-shell structure and monodisperse size distribution. Three methods to trigger cargo release have been demonstrated, namely temperature treatment, ultrasonication and pH shift. Steroidal drug dexamethasone was used to illustrate the applicability of the systems for triggered drug release. The application of proposed asymmetric capsules includes but is not limited to pharmacology, diagnostics, sensors, micro- and nanoreactors and chemical actuators.

Persistent red blood cells retain their ability to move in microcapillaries under high levels of oxidative stress.

Oxidative stress is one of the key factors that leads to red blood cells (RBCs) aging, and impairs their biomechanics and oxygen delivery. It occurs during numerous pathological processes and causes anaemia, one of the most frequent side effects of cancer chemotherapy. Here, we used microfluidics to simulate the microcirculation of RBCs under oxidative stress induced by tert-Butyl hydroperoxide. Oxidative stress was expected to make RBCs more rigid, which would lead to decrease their transit velocity in microfluidic channels. However, single-cell tracking combined with cytological and AFM studies reveals cell heterogeneity, which increases with the level of oxidative stress. The data indicates that the built-in antioxidant defence system has a limit exceeding which haemoglobin oxidation, membrane, and cytoskeleton transformation occurs. It leads to cell swelling, increased stiffness and adhesion, resulting in a decrease in the transit velocity in microcapillaries. However, even at high levels of oxidative stress, there are persistent cells in the population with an undisturbed biophysical phenotype that retain the ability to move in microcapillaries. Developed microfluidic analysis can be used to determine RBCs' antioxidant capacity for the minimization of anaemia during cancer chemotherapy.

Nanomechanical characterization of exosomes and concomitant nanoparticles from blood plasma by PeakForce AFM in liquid.

BACKGROUND: To date, EVs characterization techniques are extremely diverse. The contribution of AFM, in particular, is often confined to size distribution. While AFM provides a unique possibility to carry out measurements in situ, nanomechanical characterization of EVs is still missing. METHODS: Blood plasma EVs were isolated by ultracentrifugation, analyzed by flow cytometry and NTA. Followed by cryo-EM, we applied PeakForce AFM to assess morphological and nanomechanical properties of EVs in liquid. RESULTS: Nanoparticles were subdivided by their size estimated for their suspended state into sub-sets of small S1-EVs (< 30 nm), S2-EVs (30-50 nm), and sub-set of large ones L-EVs (50-170 nm). Non-membranous S1-EVs were distinguished by higher Young's modulus (10.33(7.36;15.25) MPa) and were less deformed by AFM tip (3.6(2.8;4.4) nm) compared to membrane exosomes S2-EVs (6.25(4.52;8.24) MPa and 4.8(4.3;5.9) nm). L-EVs were identified as large membrane exosomes, heterogeneous by their nanomechanical properties (22.43(8.26;53.11) MPa and 3.57(2.07;7.89) nm). Nanomechanical mapping revealed a few non-deformed L-EVs, of which Young's modulus rose up to 300 MPa. Taken together with cryo-EM, these results lead us to the suggestion that two or more vesicles could be contained inside a large one being a multilayer vesicle. CONCLUSIONS: We identified particles similar in morphology and showed differences in nanomechanical properties that could be attributed to the features of their inner structure. GENERAL SIGNIFICANCE: Our results further elucidate the identification of EVs and concomitant nanoparticles based on their nanomechanical properties.

Incorporation of Perovskite Nanocrystals into Polymer Matrix for Enhanced Stability in Biological Media: In Vitro and In Vivo Studies.

The outstanding optical properties and multiphoton absorption of lead halide perovskites make them promising for use as fluorescence tags in bioimaging applications. However, their poor stability in aqueous media and biological fluids significantly limits their further use for in vitro and in vivo applications. In this work, we have developed a universal approach for the encapsulation of lead halide perovskite nanocrystals (PNCs) (CsPbBr3 and CsPbI3) as water-resistant fluorescent markers, which are suitable for fluorescence bioimaging. The obtained encapsulated PNCs demonstrate bright green emission at 510 nm (CsPbBr3) and red emission at 688 nm (CsPbI3) under one- and two-photon excitation, and they possess an enhanced stability in water and biological fluids (PBS, human serum) for a prolonged period of time (1 week). Further in vitro and in vivo experiments revealed enhanced stability of PNCs even after their introduction directly into the biological microenvironment (CT26 cells and DBA mice). The developed approach allows making a step toward stable, low-cost, and highly efficient bioimaging platforms that are spectrally tunable and have narrow emission.

Droplet Microfluidic Device for Chemoenzymatic Sensing.

The rapid detection of pollutants in water can be performed with enzymatic probes, the catalytic light-emitting activity of which decreases in the presence of many types of pollutants. Herein, we present a microfluidic system for continuous chemoenzymatic biosensing that generates emulsion droplets containing two enzymes of the bacterial bioluminescent system (luciferase and NAD(P)H:FMN-oxidoreductase) with substrates required for the reaction. The developed chip generates "water-in-oil" emulsion droplets with a volume of 0.1 µL and a frequency of up to 12 drops per minute as well as provides the efficient mixing of reagents in droplets and their distancing. The bioluminescent signal from each individual droplet was measured by a photomultiplier tube with a signal-to-noise ratio of up to 3000/1. The intensity of the luminescence depended on the concentration of the copper sulfate with the limit of its detection of 5 µM. It was shown that bioluminescent enzymatic reactions could be carried out in droplet reactors in dispersed streams. The parameters and limitations required for the bioluminescent reaction to proceed were also studied. Hereby, chemoenzymatic sensing capabilities powered by a droplet microfluidics manipulation technique may serve as the basis for early-warning online water pollution systems.

Negative Pressure Provides Simple and Stable Droplet Generation in a Flow-Focusing Microfluidic Device.

Droplet microfluidics is an extremely useful and powerful tool for industrial, environmental, and biotechnological applications, due to advantages such as the small volume of reagents required, ultrahigh-throughput, precise control, and independent manipulations of each droplet. For the generation of monodisperse water-in-oil droplets, usually T-junction and flow-focusing microfluidic devices connected to syringe pumps or pressure controllers are used. Here, we investigated droplet-generation regimes in a flow-focusing microfluidic device induced by the negative pressure in the outlet reservoir, generated by a low-cost mini diaphragm vacuum pump. During the study, we compared two ways of adjusting the negative pressure using a compact electro-pneumatic regulator and a manual airflow control valve. The results showed that both types of regulators are suitable for the stable generation of monodisperse droplets for at least 4 h, with variations in diameter less than 1 µm. Droplet diameters at high levels of negative pressure were mainly determined by the hydrodynamic resistances of the inlet microchannels, although the absolute pressure value defined the generation frequency; however, the electro-pneumatic regulator is preferable and convenient for the accurate control of the pressure by an external electric signal, providing more stable pressure, and a wide range of droplet diameters and generation frequencies. The method of droplet generation suggested here is a simple, stable, reliable, and portable way of high-throughput production of relatively large volumes of monodisperse emulsions for biomedical applications.

Experimental Platform to Study Spiking Pattern Propagation in Modular Networks In Vitro.

The structured organization of connectivity in neural networks is associated with highly efficient information propagation and processing in the brain, in contrast with disordered homogeneous network architectures. Using microfluidic methods, we engineered modular networks of cultures using dissociated cells with unidirectional synaptic connections formed by asymmetric microchannels. The complexity of the microchannel geometry defined the strength of the synaptic connectivity and the properties of spiking activity propagation. In this study, we developed an experimental platform to study the effects of synaptic plasticity on a network level with predefined locations of unidirectionally connected cellular assemblies using multisite extracellular electrophysiology.

Microfluidic Characterization of Red Blood Cells Microcirculation under Oxidative Stress.

Microcirculation is one of the basic functional processes where the main gas exchange between red blood cells (RBCs) and surrounding tissues occurs. It is greatly influenced by the shape and deformability of RBCs, which can be affected by oxidative stress induced by different drugs and diseases leading to anemia. Here we investigated how in vitro microfluidic characterization of RBCs transit velocity in microcapillaries can indicate cells damage and its correlation with clinical hematological analysis. For this purpose, we compared an SU-8 mold with an Si-etched mold for fabrication of PDMS microfluidic devices and quantitatively figured out that oxidative stress induced by tert-Butyl hydroperoxide splits all RBCs into two subpopulations of normal and slow cells according to their transit velocity. Obtained results agree with the hematological analysis showing that such changes in RBCs velocities are due to violations of shape, volume, and increased heterogeneity of the cells. These data show that characterization of RBCs transport in microfluidic devices can directly reveal violations of microcirculation caused by oxidative stress. Therefore, it can be used for characterization of the ability of RBCs to move in microcapillaries, estimating possible side effects of cancer chemotherapy, and predicting the risk of anemia.

Biomechanical Properties of Blood Plasma Extracellular Vesicles Revealed by Atomic Force Microscopy.

While extracellular vesicles (EVs) are extensively studied by various practical applications in biomedicine, there is still little information on their biomechanical properties due to their nanoscale size. We identified isolated blood plasma vesicles that carried on biomarkers associated with exosomes and exomeres and applied atomic force microscopy (AFM) to study them at single particle level in air and in liquid. Air measurements of exosomes revealed a mechanically indented internal cavity in which highly adhesive sites were located. In contrast, the highly adhesive sites of exomeres were located at the periphery and the observed diameter of the particles was ~35 nm. In liquid, the reversible deformation of the internal cavity of exosomes was observed and a slightly deformed lipid bi-layer was identified. In contrast, exomeres were not deformed and their observed diameter was ~16 nm. The difference in diameters might be associated with a higher sorption of water film in air. The parameters we revealed correlated with the well-known structure and function for exosomes and were observed for exomeres for the first time. Our data provide a new insight into the biomechanical properties of nanoparticles and positioned AFM as an exclusive source of in situ information about their biophysical characteristics.

A highly efficient and safe gene delivery platform based on polyelectrolyte core-shell nanoparticles for hard-to-transfect clinically relevant cell types.

While DNA and messenger RNA (mRNA) based therapies are currently changing the biomedical field, the delivery of genetic materials remains the key problem preventing the wide introduction of these methods into clinical practice. Therefore, the creation of new methods for intracellular gene delivery, particularly to hard-to-transfect, clinically relevant cell populations is a pressing issue. Here, we report on the design of a novel approach to format 50-150 nm calcium carbonate particles in the vaterite state and using them as a template for polymeric core-shell nanoparticles. We apply such core-shell nanoparticles as safe and efficient carriers for mRNA and pDNA. We prove that such nanocarriers are actively internalized by up to 99% of primary T-lymphocytes and exert minimal toxicity with the viability of >90%. We demonstrate that these nanocarriers mediate more efficient transfection compared with the standard electroporation method (90% vs. 51% for mRNA and 62% vs. 39% for plasmid DNA) in primary human T-lymphocytes as a model of the hard to transfect type that is widely used in gene and cell therapy approaches. Importantly, these polymeric nanocarriers can be used in serum containing basic culture medium without special conditions and equipment, thus having potential for being introduced in clinical development. As a result, we have provided proof-of-principle that our nanosized containers represent a promising universal non-viral platform for efficient and safe gene delivery.

Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor.

Background: The ability of ErbB3 receptor to functionally complement ErbB1-2 and induce tumor resistance to their inhibitors makes it a unique target in cancer therapy by monoclonal antibodies. Here we report the expression, purification and structural analysis of a new anti-ErbB3 single-chain antibody. Methods: The VHH fragment of the antibody was expressed in E. coli SHuffle cells as a SUMO fusion, cleaved by TEV protease and purified to homogeneity. Binding to the extracellular domain of ErbB3 was studied by surface plasmon resonance. For structural studies, the antibody was crystallized by hanging-drop vapor diffusion in two different forms. Results: We developed a robust and efficient system for recombinant expression of single-domain antibodies. The purified antibody was functional and bound ErbB3 with K D =15±1 nM. The crystal structures of the VHH antibody in space groups C2 and P1 were solved by molecular replacement at 1.6 and 1.9 Å resolution. The high-quality electron density maps allowed us to build precise atomic models of the antibody and the putative paratope. Surprisingly, the CDR H2 existed in multiple distant conformations in different crystal forms, while the more complex CDR H3 had a low structural variability. The structures were deposited under PDB entry codes 6EZW and 6F0D. Conclusions: Our results may facilitate further mechanistic studies of ErbB3 inhibition by single-chain antibodies. Besides, the solved structures will contribute to datasets required to develop new computational methods for antibody modeling and design.