Interpretable unsupervised learning enables accurate clustering with high-throughput imaging flow cytometry.

A primary challenge of high-throughput imaging flow cytometry (IFC) is to analyze the vast amount of imaging data, especially in applications where ground truth labels are unavailable or hard to obtain. We present an unsupervised deep embedding algorithm, the Deep Convolutional Autoencoder-based Clustering (DCAEC) model, to cluster label-free IFC images without any prior knowledge of input labels. The DCAEC model first encodes the input images into the latent representations and then clusters based on the latent representations. Using the DCAEC model, we achieve a balanced accuracy of 91.9% for human white blood cell (WBC) clustering and 97.9% for WBC/leukemia clustering using the 3D IFC images and 3D DCAEC model. Above all, although no human recognizable features can separate the clusters of cells with protein localization, we demonstrate the fused DCAEC model can achieve a cluster balanced accuracy of 85.3% from the label-free 2D transmission and 3D side scattering images. To reveal how the neural network recognizes features beyond human ability, we use the gradient-weighted class activation mapping method to discover the cluster-specific visual patterns automatically. Evaluation results show that the automatically identified salient image regions have strong cluster-specific visual patterns for different clusters, which we believe is a stride for the interpretable neural network for cell analysis with high-throughput IFCs.

Tribocorrosion Behavior of Micro/Nanoscale Surface Coatings.

Wear and corrosion are common issues of material degradation and failure in industrial appliances. Wear is a damaging process that can impact surface contacts and, more specifically, can cause the loss and distortion of material from a surface because of the contacting object's mechanical action via motion. More wear occurs during the process of corrosion, in which oxide particles or debris are released from the contacting material. These types of wear debris and accumulated oxide particles released during corrosion cause a combination of wear-corrosion processes. Bringing together the fields of tribology and corrosion research, tribocorrosion is a field of study which deals with mechanical and electrochemical interactions between bodies in motion. More specifically, it is the study of mechanisms caused by the combined effects of mechanical stress and chemical/electrochemical interactions with the environment. Tribocorrosion testing methods provide new opportunities for studying the electrochemical nature of corrosion combined with mechanical loading to establish a synergistic relationship between corrosion and wear. To improve tribological, mechanical, and anti-corrosion performances, several surface modification techniques are being applied to develop functional coatings with micro/nano features. This review of the literature explores recent and enlightening research into the tribocorrosive properties of micro/nano coatings. It also looks at recent discussions of the most common experimental methods and some newer, promising experimental methods in tribocorrosion to elucidate their applications in the field of micro/nano coatings.

Label-free image-encoded microfluidic cell sorter with a scanning Bessel beam.

The microfluidic-based, label-free image-guided cell sorter offers a low-cost, high information content, and disposable solution that overcomes many limitations in conventional cell sorters. However, flow confinement for most microfluidic devices is generally only one-dimensional using sheath flow. As a result, the equilibrium distribution of cells spreads beyond the focal plane of commonly used Gaussian laser excitation beams, resulting in a large number of blurred images that hinder subsequent cell sorting based on cell image features. To address this issue, we present a Bessel-Gaussian beam image-guided cell sorter with an ultra-long depth of focus, enabling focused images of >85% of passing cells. This system features label-free sorting capabilities based on features extracted from the output temporal waveform of a photomultiplier tube (PMT) detector. For the sorting of polystyrene beads, SKNO1 leukemia cells, and Scenedesmus green algae, our results indicate a sorting purity of 97%, 97%, and 98%, respectively, showing that the temporal waveforms from the PMT outputs have strong correlations with cell image features. These correlations are also confirmed by off-line reconstructed cell images from a temporal-spatial transformation algorithm tailored to the scanning Bessel-Gaussian beam.

Dependence of Membrane Tether Strength on Substrate Rigidity Probed by Single-Cell Force Spectroscopy.

Substrate rigidity modulates cell mechanics, which affect cell migration and proliferation. Quantifying the effects of substrate rigidity on cancer cell mechanics requires a quantifiable parameter that can be measured for individual cells, as well as a substrate platform with rigidity being the only variable. Here we used single-cell force spectroscopy to pull cancer cells on substrates varying only in rigidity, and extracted a parameter from the force-distance curves to be used to quantify the properties of membrane tethers. Our results showed that tether force increases with substrate rigidity until it reaches its asymptotic limit. The variations are similar for all three cancer cell lines studied, and the largest change occurs in the rigidity regions of softer tissues, indicating a universal response of cancer cell elasticity to substrate rigidity.

A Novel Technique Enables Quantifying the Molecular Interaction of Solvents with Biological Tissues.

The pharmaceutical industry uses various solvents to increase drug penetrability to tissues. The solvent's choice affects the efficacy of a drug. In this paper, we provide an unprecedented means of relating a solvent to a tissue quantitatively. We show that the solvents induce reorientation of the tissue surface molecules in a way that favors interaction and, therefore, penetrability of a solvent to a tissue. We provide, for the first time, a number for this tendency through a new physical property termed Interfacial Modulus (Gs). Gs, which so far was only predicted theoretically, is inversely proportional to such interactions. As model systems, we use HeLa and HaCaT tissue cultures with water and with an aqueous DMSO solution. The measurements are done using Centrifugal Adhesion Balance (CAB) when set to effective zero gravity. As expected, the addition of DMSO to water reduces Gs. This reduction in Gs is usually higher for HaCaT than for HeLa cells, which agrees with the common usage of DMSO in dermal medicine. We also varied the rigidities of the tissues. The tissue rigidity is not expected to relate to Gs, and indeed our results didn't show a correlation between these two physical properties.

Rapid Waterborne Pathogen Detection with Mobile Electronics.

Pathogen detection in water samples, without complex and time consuming procedures such as fluorescent-labeling or culture-based incubation, is essential to public safety. We propose an immunoagglutination-based protocol together with the microfluidic device to quantify pathogen levels directly from water samples. Utilizing ubiquitous complementary metal-oxide-semiconductor (CMOS) imagers from mobile electronics, a low-cost and one-step reaction detection protocol is developed to enable field detection for waterborne pathogens. 10 mL of pathogen-containing water samples was processed using the developed protocol including filtration enrichment, immune-reaction detection and imaging processing. The limit of detection of 10 E. coli O157:H7 cells/10 mL has been demonstrated within 10 min of turnaround time. The protocol can readily be integrated into a mobile electronics such as smartphones for rapid and reproducible field detection of waterborne pathogens.

Protein-Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies.

Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions. Through experiments and theoretical simulations, we demonstrate that the TIMES technique actually detects protein-ligand binding through signals generated by surface electric polarization. The accuracy and sensitivity of experiments were demonstrated by precise measurements of dissociation constant of lysozyme and N-acetyl-d-glucosamine (NAG) ligand and its trimer, NAG3. Computational fluid dynamics (CFD) computation is performed to demonstrate that the surface's electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization to give the characteristic TIMES signals. Although the current work is focused on protein-ligand interactions, the TIMES method is a general technique that can be applied to study signals from reactions between many kinds of molecules.

A Single-Cell Assay for Time Lapse Studies of Exosome Secretion and Cell Behaviors.

To understand the inhomogeneity of cells in biological systems, there is a growing demand on the capability of characterizing the properties of individual single cells. Since single-cell studies require continuous monitoring of the cell behaviors, an effective single-cell assay that can support time lapsed studies in a high throughput manner is desired. Most currently available single-cell technologies cannot provide proper environments to sustain cell growth and, proliferation of single cells and convenient, noninvasive tests of single-cell behaviors from molecular markers. Here, a highly versatile single-cell assay is presented that can accommodate different cellular types, enable easy and efficient single-cell loading and culturing, and be suitable for the study of effects of in vitro environmental factors in combination with drug screening. One salient feature of the assay is the noninvasive collection and surveying of single-cell secretions at different time points, producing unprecedented insight of single-cell behaviors based on the biomarker signals from individual cells under given perturbations. Above all, the acquired information is quantitative, for example, measured by the number of exosomes each single-cell secretes for a given time period. Therefore, our single-cell assay provides a convenient, low-cost, and enabling tool for quantitative, time lapsed studies of single-cell properties.

Self-Assembled Pico-Liter Droplet Microarray for Ultrasensitive Nucleic Acid Quantification.

Nucleic acid detection and quantification technologies have made remarkable progress in recent years. Among existing platforms, hybridization-based assays have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, we developed a quantitative physical model for the hybridization-based assay to guide the experimental design, which leads to a pico-liter droplet environment with drastically enhanced performance and detection limit several order above any current microarray platform. The pico-liter droplet hybridization platform is further coupled with the on-chip enrichment technique to yield ultrahigh sensitivity both in terms of target concentration and copy number. Our physical model, taking into account of molecular transport, electrostatic intermolecular interactions, reaction kinetics, suggests that reducing liquid height and optimizing target concentration will maximize the hybridization efficiency, and both conditions can be satisfied in a highly parallel, self-assembled pico-liter droplet microarray that produces a detection limit as low as 570 copies and 50 aM. The pico-liter droplet array device is realized with a micropatterned superhydrophobic black silicon surface that allows enrichment of nucleic acid samples by position-defined evaporation. With on-chip enrichment and oil encapsulated pico-liter droplet arrays, we have demonstrated a record high sensitivity, wide dynamic range (6 orders of magnitude), and marked reduction of hybridization time from >10 h to <5 min in a highly repeatable fashion, benefiting from the physics-driven design and nanofeatures of the device. The design principle and technology can contribute to biomedical sensing and point-of-care clinical applications such as pathogen detection and cancer diagnosis and prognosis.

A gp130-Src-YAP module links inflammation to epithelial regeneration.

Inflammation promotes regeneration of injured tissues through poorly understood mechanisms, some of which involve interleukin (IL)-6 family members, the expression of which is elevated in many diseases including inflammatory bowel diseases and colorectal cancer. Here we show in mice and human cells that gp130, a co-receptor for IL-6 cytokines, triggers activation of YAP and Notch, transcriptional regulators that control tissue growth and regeneration, independently of the gp130 effector STAT3. Through YAP and Notch, intestinal gp130 signalling stimulates epithelial cell proliferation, causes aberrant differentiation and confers resistance to mucosal erosion. gp130 associates with the related tyrosine kinases Src and Yes, which are activated on receptor engagement to phosphorylate YAP and induce its stabilization and nuclear translocation. This signalling module is strongly activated upon mucosal injury to promote healing and maintain barrier function.

Oil-encapsulated nanodroplet array for bio-molecular detection.

Detection of low abundance biomolecules is challenging for biosensors that rely on surface chemical reactions. For surface reaction based biosensors, it require to take hours or even days for biomolecules of diffusivities in the order of 10(-10-11) m2/s to reach the surface of the sensors by Brownian motion. In addition, often times the repelling Coulomb interactions between the molecules and the probes further defer the binding process, leading to undesirably long detection time for applications such as point-of-care in vitro diagnosis. In this work, we designed an oil encapsulated nanodroplet array microchip utilizing evaporation for pre-concentration of the targets to greatly shorten the reaction time and enhance the detection sensitivity. The evaporation process of the droplets is facilitated by the superhydrophilic surface and resulting nanodroplets are encapsulated by oil drops to form stable reaction chamber. Using this method, desirable droplet volumes, concentrations of target molecules, and reaction conditions (salt concentrations, reaction temperature, etc.) in favour of fast and sensitive detection are obtained. A linear response over 2 orders of magnitude in target concentration was achieved at 10 fM for protein targets and 100 fM for miRNA mimic oligonucleotides.

Regulation of the Hippo-YAP pathway by G-protein-coupled receptor signaling.

The Hippo pathway is crucial in organ size control, and its dysregulation contributes to tumorigenesis. However, upstream signals that regulate the mammalian Hippo pathway have remained elusive. Here, we report that the Hippo pathway is regulated by G-protein-coupled receptor (GPCR) signaling. Serum-borne lysophosphatidic acid (LPA) and sphingosine 1-phosphophate (S1P) act through G12/13-coupled receptors to inhibit the Hippo pathway kinases Lats1/2, thereby activating YAP and TAZ transcription coactivators, which are oncoproteins repressed by Lats1/2. YAP and TAZ are involved in LPA-induced gene expression, cell migration, and proliferation. In contrast, stimulation of Gs-coupled receptors by glucagon or epinephrine activates Lats1/2 kinase activity, thereby inhibiting YAP function. Thus, GPCR signaling can either activate or inhibit the Hippo-YAP pathway depending on the coupled G protein. Our study identifies extracellular diffusible signals that modulate the Hippo pathway and also establishes the Hippo-YAP pathway as a critical signaling branch downstream of GPCR.

The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation.

Yes-associated protein (YAP) is a potent transcription coactivator acting via binding to the TEAD transcription factor, and plays a critical role in organ size regulation. YAP is phosphorylated and inhibited by the Lats kinase, a key component of the Hippo tumor suppressor pathway. Elevated YAP protein levels and gene amplification have been implicated in human cancer. In this study, we report that YAP is inactivated during embryonic stem (ES) cell differentiation, as indicated by decreased protein levels and increased phosphorylation. Consistently, YAP is elevated during induced pluripotent stem (iPS) cell reprogramming. YAP knockdown leads to a loss of ES cell pluripotency, while ectopic expression of YAP prevents ES cell differentiation in vitro and maintains stem cell phenotypes even under differentiation conditions. Moreover, YAP binds directly to promoters of a large number of genes known to be important for stem cells and stimulates their expression. Our observations establish a critical role of YAP in maintaining stem cell pluripotency.

Mouse erythrocyte tropomodulin in the brain reported by lacZ knocked-in downstream from the E1 promoter.

Erythrocyte tropomodulin (E-Tmod, Tmod1) is a tropomyosin-binding protein that caps the slow-growing end of actin filaments. In erythrocytes, it may favor the formation of short actin protofilaments needed for elastic cell deformation. Previously we created a knockout mouse model in which lacZ was knocked-in downstream of the E1 promoter to report the expression of full length E-Tmod. Here we utilize E-Tmod(+/lacZ) mice to study E-Tmod expression patterns in the CNS. X-gal staining and in situ hybridization of adults revealed its restricted expression in the olfactory bulb, hippocampus, cerebral cortex, basal ganglia, nuclei of brain stem and cerebellum. In neonates, signals in the cortex and caudate putamen increased from days 15 to 40. Immunohistochemistry also revealed that signals for beta-galactosidase coincided with that of NeuN, a post-mitotic nuclear marker for neurons, but not that for GFAP+ astrocytes or APC+ oligodendrocytes, suggesting E-Tmod/lacZ-positive cells in the CNS were neurons. Large neurons, e.g., mitral cells in olfactory bulb and mossy cells in hilus of the dentate gyrus are among those that expressed very high levels of E-Tmod in the CNS.

Roles of MAP kinases in the regulation of bone matrix gene expressions in human osteoblasts by oscillatory fluid flow.

We investigated the effects of oscillatory flow in regulating the gene expressions of type I collagen (COL1, the main component of human bone tissues) and osteopontin (OPN, the key gene for calcium deposition) in human osteoblast-like (MG-63) cells, and the roles of mitogen-activated protein kinases (MAPKs) in this regulation. The cells were subjected to oscillatory flow (0.5 +/- 4 dyn/cm(2)) or kept under static condition for various time periods (15 min, 30 min, 1 h, 2 h, 4 h, 8 h, and 16 h). Oscillatory flow caused significant up-regulations of both COL1 and OPN gene expressions over the 16 h of study, and a transient activation of MAPKs was starting at 15 min and declining to basal level in 2 h. The flow-induction of COL1 was blocked by an ERK inhibitor (PD98059) and reduced by a JNK inhibitor (SP600125), whereas that of OPN was abolished by PD98059. Analysis of the cis-elements in the COL1 and OPN promoters suggests the involvement of transacting factors Elk-1 and AP-1 in the transcription regulation. The ERK inhibitor (PD98059) blocked Elk-1 phosphorylation, as well as COL1 and OPN gene expression. The JNK inhibitor (SP600125) abolished c-jun phosphorylation and COL1 expression. These results suggest that the flow-induction of OPN was mediated through the ERK-Elk1-OPN pathway, and that COL1 was regulated by both the ERK-Elk1-COL1 and JNK-c-JUN-COL1 pathway.

DNA microarray study on gene expression profiles in co-cultured endothelial and smooth muscle cells in response to 4- and 24-h shear stress.

Shear stress, a major hemodynamic force acting on the vessel wall, plays an important role in physiological processes such as cell growth, differentiation, remodelling, metabolism, morphology, and gene expression. We investigated the effect of shear stress on gene expression profiles in co-cultured vascular endothelial cells (ECs) and smooth muscle cells (SMCs). Human aortic ECs were cultured as a confluent monolayer on top of confluent human aortic SMCs, and the EC side of the co-culture was exposed to a laminar shear stress of 12 dyn/cm(2) for 4 or 24 h. After shearing, the ECs and SMCs were separated and RNA was extracted from the cells. The RNA samples were labelled and hybridized with cDNA array slides that contained 8694 genes. Statistical analysis showed that shear stress caused the differential expression (p < or = 0.05) of a total of 1151 genes in ECs and SMCs. In the co-cultured ECs, shear stress caused the up-regulation of 403 genes and down-regulation of 470. In the co-cultured SMCs, shear stress caused the up-regulation of 152 genes and down-regulation of 126 genes. These results provide new information on the gene expression profile and its potential functional consequences in co-cultured ECs and SMCs exposed to a physiological level of laminar shear stress. Although the effects of shear stress on gene expression in monocultured and co-cultured EC are generally similar, the response of some genes to shear stress is opposite between these two types of culture (e.g., ICAM-1 is up-regulated in monoculture and down-regulated in co-culture), which strongly indicates that EC-SMC interactions affect EC responses to shear stress.