Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

Reducing the use of animal models in drug development and safety assessment has long been supported by the U.S.Food and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million animals.Beyond ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug exposure.While animal testing has been the traditional method for assessing the safety and efficacy of drugs.

REDUCTION IN PERITONITIS INCIDENCE IN CONTINUOUS AMBULATORY PERITONEAL DIALYSIS WITH A NEW CATHETER AND IMPLANTATION TECHNIQUE

Recurrent episodes of peritonitis with the same organism cultured at thecatheter exit site suggest that early tunnel colonization is associated with a transferof these organisms through the catheter tunnel directly from the skin into the peri-toneal cavity.In this circumstance the catheter has failed in its fundamental designto establish and maintain a bacteriological barrier.A three part study was conductedusing the Moncrief-Popovich Catheter and Implantation Technique.The first part

Osteogenesis of MC3T3 Preosteoblasts on 3D Bioactive Peptide Modified Nano-Macroporous Bioactive Glass Scaffolds

Biointerface design that targets osteogenesis is a growing area of research with significant implications in biomedicine. Materials known to either support or stimulate osteogenesis are composed of a biomimetic ceramic material, such as bioactive glass. Bioactive glass is osteoproductive, and the potential for osteoproductivity can be enhanced by the addition of proteins or other additives designed to alter functionality. In addition, soluble growth factors are often added to osteogenic culture on bioactive glasses, further intensifying the effects of the material. In this paper, synthetic peptide combinations, covalently bound to a three-dimensional bioactive glass network, are used to mimic the effects of the whole fibronectin and bone morphogenetic proteins (BMP) 2 and 9. Peptide-silanes possessing critical binding sequences from each of these proteins are synthesized and used to decorate the surface of three-dimensional (3D) nano-macroporous bioactive glass. MC3T3 preosteoblast cells are then assessed for differentiation on the materials in the absence of soluble differentiation cues. MC3T3 preosteoblasts undergo enhanced differentiation on the peptide-silane samples over the standard nano-macroporous bioactive glass, and the differentiation capacity of the cells exposes only to peptide-silane surfaces approaches that of cells grown in chemical differentiation induction media.

Mechanistic modeling of copper corrosions in data center environments

Air-side economizers are increasingly used to take advantage of“free-cooling”in data centers with the intent of reducing the carbon footprint of buildings.However,they can introduce outdoor pollutants to indoor environment of data centers and cause corrosion damage to the information technology equipment.To evaluate the reliability of information technology equipment under various thermal and air-pollution conditions,a mechanistic model based on multi-ion transport and chemical reactions was developed.The model was used to predict Cu corrosion caused by Cl_(2)-containing pollutant mixtures.It also accounted for the effects of temperature(25℃and 28℃),relative humidity(50%,75%,and 95%),and synergism.It also identified higher air temperature as a corrosion barrier and higher relative humidity as a corrosion accelerator,which agreed well with the experimental results.The average root mean square error of the prediction was 13.7Å.The model can be used to evaluate the thermal guideline for data centers design and operation when Cl_(2)is present based on pre-established acceptable risk of corrosion in data centers’environment.

Visualizing hypoxic modulation of beta cell secretions via a sensor augmented oxygen gradient

One distinct advantage of microfluidic-based cell assays is their scalability for multiple concentrations or gradients.Microfluidic scaling can be extremely powerful when combining multiple parameters and modalities.Moreover,in situ stimulation and detection eliminates variability between individual bioassays.However,conventional microfluidics must combat diffusion,which limits the spatial distance and time for molecules traveling through microchannels.Here,we leveraged a multilayered microfluidic approach to integrate a novel oxygen gradient(0–20%)with an enhanced hydrogel sensor to study pancreatic beta cells.This enabled our microfluidics to achieve spatiotemporal detection that is difficult to achieve with traditional microfluidics.Using this device,we demonstrated the in situ detection of calcium,insulin,and ATP(adenosine triphosphate)in response to glucose and oxygen stimulation.Specifically,insulin was quantified at levels as low as 25 pg/mL using our imaging technique.Furthermore,by analyzing the spatial detection data dynamically over time,we uncovered a new relationship between oxygen and beta cell oscillations.We observed an optimum oxygen level between 10 and 12%,which is neither hypoxic nor normoxic in the conventional cell culture sense.These results provide evidence to support the current islet oscillator model.In future applications,this spatial microfluidic technique can be adapted for discrete protein detection in a robust platform to study numerous oxygen-dependent tissue dysfunctions.

Mitochondria-derived small RNAs as diagnostic biomarkers in lung cancer patients through a novel ratio-based expression analysis methodology

Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Currently, there are no reports of studies of mtRNA in human lung cancer. Currently, normalization methods are unstable, and they often fail to identify differentially expressed small non-coding RNAs (sncRNAs). In order to identify reliable biomarkers for lung cancer screening, we used a ratio-based method using mtRNAs newly discovered in human peripheral blood mononuclear cells. In the discovery cohort (AUC = 0.981) and independent validation cohort (AUC = 0.916) the prediction model of eight mtRNA ratios distinguished lung cancer patients from controls. The prediction model will provide reliable biomarkers that will allow blood-based screening to become more feasible and will help make lung cancer diagnosis more accurate in clinical practice.

Synthesis of an AIE-active fluorogen and its application in cell imaging

A fluorogen named 1-decyl-1-methyl-2,5-bis{4-[(N,N-diethylamino)methyl]phenyl}-3,4-diphenylsilole (3) was synthesized. It emitted weakly as isolated molecule but strongly as supramolecular aggregate, showing a characteristic behavior of aggregation-induced emission (AIE). The molecules of 3 formed highly emissive nanoparticles in aqueous media, which quickly and selectively marked cytoplasm of HeLa cells and posed no toxicity to the living cells. The fluorogen is thus a promising candidate mate-rial for cell imaging as a sensitive, selective and cytocompatible biosensor.

Ultrasonic-assisted Synthesis of Fe Nanoparticles in the Presence of Poly（N-vinyl-2-pyrrolidone）

Zero-valent iron particles were prepared by wet reduction chemistry assisted with ultrasonic treatment. Such prepared particles have uniform size, exhibit crystalline structure and show strong pararnagnetic property. Their surface modification by coating poly（N-vinyl-2-pyrrolidone） （PVP） was investigated. The resulting Fe（0）-PVP particles were monodispersed and possessed enhancing magnetization saturation. Those synthesis conditions to control the particle size and distribution were exploited.

Digital holographic microscopy with phase-shift-free structured illumination

When structured illumination is used in digital holographic microscopy(DHM),each direction of the illumination fringe is required to be shifted at least three times to perform the phase-shifting reconstruction.In this paper,we propose a scheme for spatial resolution enhancement of DHM by using the structured illumination but without phase shifting.The structured illuminations of different directions,which are generated by a spatial light modulator,illuminate the sample sequentially in the object plane.The formed object waves interfere with a reference wave in an off-axis configuration,and a CCD camera records the generated hologram.After the object waves are reconstructed numerically,a synthetic aperture is performed by an iterative algorithm to enhance the spatial resolution.The resolution improvement of the proposed method is proved and demonstrated by both simulation and experiment.

uorescence microendoscopy imaging based on GRIN lenses with one- and two-photon excitation modes

With the rapid development of life sciences, there is an increasing demand for intravital fluorescence imaging of small animals. However, large dimensions and limited working distances of objective lenses in traditional fluorescence microscopes have limited their imaging applications mostly to superficial tissues. To overcome these disadvantages, researchers have developed the graded-index （GRIN） probes with small diameters for imaging internal organs of small animals in a minimally invasive fashion. However, dynamic imaging based on GRIN lens has not been studied extensively. Here, this paper presented a fluorescence endoscopic imaging system based on GRiN lenses using one-photon and two-photon excitation. GRIN lenses with 1.15 mm diameter and 7.65 mm length were used in the system. The images were acquired by a compact laser scanning imaging system with a resonant galvo-mirror system to scan the laser beam and a photomultiplier tube （PMT） to detect fluorescence signals. Experimental results showed that this system using two-photon excitation could implement dynamic fluorescence microendoscopic imaging and monitor the movement of blood flow beneath the skin in anesthetized mice while producing images with higher contrast and signal to noise ratio （SNR） than those using one photon excitation. It would be a useful tool for studying biological processes of small animals or plants in vivo.

Morphology of living cells cultured on nanowire arrays with varying nanowire densities and diameters

Vertical nanowire arrays are increasingly investigated for their applications in steering cell behavior. The geometry of the array is an important parameter, which influences the morphology and adhesion of cells. Here, we investigate the effects of array geometry on the morphology of MCF7 cancer cells and MCF10A normal-like epithelial cells. Different gallium phosphide nanowire array-geometries were produced by varying the nanowire density and diameter. Our results show that the cell size is smaller on nanowires compared to flat gallium phosphide. The cell area decreases with increasing the nanowire density on the substrate. We observed an effect of the nanowire diameter on MCF10A cells, with a decreased cell area on 40 nm diameter nanowires, compared to 60 and 80 nm diameter nanowires in high-density arrays. The focal adhesion morphology depends on the extent to which cells are contacting the substrate. For low nanowire densities and diameters, ceils are lying on the substrate and we observed large focal adhesions at the cell edges. In contrast, for high nanowire densities and diameters, cells are lying on top of the nanowires and we observed point-like focal adhesions distributed over the whole cell. Our results constitute a step towards the ability to fine-tune cell behavior on nanowire arrays.

Development of a tRNA-derived small RNA diagnostic and prognostic signature in liver cancer

Liver cancer presents divergent clinical behaviors.There remain opportunities for molecular markers to improve liver cancer diagnosis and prognosis,especially since tRNA-derived small RNAs(tsRNA)have rarely been studied.In this study,a random forests(RF)diagnostic model was built based upon tsRNA profiling of paired tumor and adjacent normal samples and validated by independent validation(IV).A LASSO model was used to developed a seven-tsRNA-based risk score signature for liver cancer prognosis.Model performance was evaluated by a receiver operating characteristic curve(ROC curve)and Precision-Recall curve(PR curve).The five-tsRNA-based RF diagnosis model had area under the receiver operating characteristic curve(AUROC)88%and area under the precision–recall curve(AUPR)87%in the discovery cohort and 87%and 86%in IV-AUROC and IV-AUPR,respectively.The seven-tsRNA-based prognostic model predicts the overall survival of liver cancer patients(Hazard Ratio 2.02,95%CI 1.36–3.00,P<0.001),independent of standard clinicopathological prognostic factors.Moreover,the model successfully categorizes patients into high-low risk groups.Diagnostic and prognostic modeling can be reliably utilized in the diagnosis of liver cancer and high-low risk classification of patients based upon tsRNA characterization.

GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data analysis.GranatumX is inspired by the interactive webtool Granatum.GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment.It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines.The architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various platforms.GranatumX can be run on the cloud or private servers and generate reproducible results.It is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench scientists.GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.

Cell-mediated and cell membrane-coated nanoparticles for drug delivery and cancer therapy

Nanotechnology-based drug delivery platforms have been developed over the last two decades because of their favorable features in terms of improved drug bioavailability and stability.Despite recent advancement in nanotechnology platforms,this approach still falls short to meet the complexity of biological systems and diseases,such as avoiding systemic side effects,manipulating biological interactions and overcoming drug resistance,which hinders the therapeutic outcomes of the NP-based drug delivery systems.To address these issues,various strategies have been developed including the use of engineered cells and/or cell membrane-coated nanocarriers.Cell membrane receptor profiles and characteristics are vital in performing therapeutic functions,targeting,and homing of either engineered cells or cell membrane-coated nanocarriers to the sites of interest.In this context,we comprehensively discuss various cell-and cell membrane-based drug delivery approaches towards cancer therapy,the therapeutic potential of these strategies,and the limitations associated with engineered cells as drug carriers and cell membrane-associated drug nanocarriers.Finally,we review various cell types and cell membrane receptors for their potential in targeting,immunomodulation and overcoming drug resistance in cancer.