Silica-Encapsulated DNA-Based Tracers for Aquifer Characterization.

Environmental tracing is a direct way to characterize aquifers, evaluate the solute transfer parameter in underground reservoirs, and track contamination. By performing multitracer tests, and translating the tracer breakthrough times into tomographic maps, key parameters such as a reservoir's effective porosity and permeability field may be obtained. DNA, with its modular design, allows the generation of a virtually unlimited number of distinguishable tracers. To overcome the insufficient DNA stability due to microbial activity, heat, and chemical stress, we present a method to encapsulated DNA into silica with control over the particle size. The reliability of DNA quantification is improved by the sample preservation with NaN3 and particle redispersion strategies. In both sand column and unconsolidated aquifer experiments, DNA-based particle tracers exhibited slightly earlier and sharper breakthrough than the traditional solute tracer uranine. The reason behind this observation is the size exclusion effect, whereby larger tracer particles are excluded from small pores, and are therefore transported with higher average velocity, which is pore size-dependent. Identical surface properties, and thus flow behavior, makes the new material an attractive tracer to characterize sandy groundwater reservoirs or to track multiple sources of contaminants with high spatial resolution.

Magnetically controlled cyclic microscale deformation of in vitro cancer invasion models.

Mechanical cues play an important role in the metastatic cascade of cancer. Three-dimensional (3D) tissue matrices with tunable stiffness have been extensively used as model systems of the tumor microenvironment for physiologically relevant studies. Tumor-associated cells actively deform these matrices, providing mechanical cues to other cancer cells residing in the tissue. Mimicking such dynamic deformation in the surrounding tumor matrix may help clarify the effect of local strain on cancer cell invasion. Remotely controlled microscale magnetic actuation of such 3D in vitro systems is a promising approach, offering a non-invasive means for in situ interrogation. Here, we investigate the influence of cyclic deformation on tumor spheroids embedded in matrices, continuously exerted for days by cell-sized anisotropic magnetic probes, referred to as µRods. Particle velocimetry analysis revealed the spatial extent of matrix deformation produced in response to a magnetic field, which was found to be on the order of 200 µm, resembling strain fields reported to originate from contracting cells. Intracellular calcium influx was observed in response to cyclic actuation, as well as an influence on cancer cell invasion from 3D spheroids, as compared to unactuated controls. Furthermore, RNA sequencing revealed subtle upregulation of certain genes associated with migration and stress, such as induced through mechanical deformation, for spheroids exposed to actuation vs. controls. Localized actuation at one side of a tumor spheroid tended to result in anisotropic invasion toward the µRods causing the deformation. In summary, our approach offers a strategy to test and control the influence of non-invasive micromechanical cues on cancer cell invasion and metastasis.

3D magnetically controlled spatiotemporal probing and actuation of collagen networks from a single cell perspective.

Cells continuously sense and react to mechanical cues from their surrounding matrix, which consists of a fibrous network of biopolymers that influences their fate and behavior. Several powerful methods employing magnetic control have been developed to assess the micromechanical properties within extracellular matrix (ECM) models hosting cells. However, many of these are limited to in-plane sensing and actuation, which does not allow the matrix to be probed within its full 3D context. Moreover, little attention has been given to factors specific to the model ECM systems that can profoundly influence the cells contained there. Here we present methods to spatiotemporally probe and manipulate extracellular matrix networks at the scale relevant to cells using magnetic microprobes (µRods). Our techniques leverage 3D magnetic field generation, physical modeling, and image analysis to examine and apply mechanical stimuli to fibrous collagen matrices. We determined shear moduli ranging between hundreds of Pa to tens of kPa and modeled the effects of proximity to rigid surfaces and local fiber densification. We analyzed the spatial extent and dynamics of matrix deformation produced in response to magnetic torques on the order of 10 pNm, deflecting fibers over an area spanning tens of micrometers. Finally, we demonstrate 3D actuation and pose extraction of fluorescently labelled µRods.

Correction: Diabetes-related changes in the protein composition and the biomechanical properties of human retinal vascular basement membranes.

[This corrects the article DOI: 10.1371/journal.pone.0189857.].

Diabetes-related changes in the protein composition and the biomechanical properties of human retinal vascular basement membranes.

Basement membranes (BMs) are specialized sheets of extracellular matrix that outline epithelial cell layers, muscle fibers, blood vessels, and peripheral nerves. A well-documented histological hallmark of progressing diabetes is a major increase in vascular BM thickness. In order to investigate whether this structural change is accompanied by a change in the protein composition, we compared the proteomes of retinal vascular BMs from diabetic and non-diabetic donors by using LC-MS/MS. Data analysis showed that seventeen extracellular matrix (ECM)-associated proteins were more abundant in diabetic than non-diabetic vascular BMs. Four ECM proteins were more abundant in non-diabetic than in diabetic BMs. Most of the over-expressed proteins implicate a complement-mediated chronic inflammatory process in the diabetic retinal vasculature. We also found an up-regulation of norrin, a protein that is known to promote vascular proliferation, possibly contributing to the vascular remodeling during diabetes. Many of the over-expressed proteins were localized to microvascular aneurisms. Further, the overall stoichiometry of proteins was changed, such that the relative abundance of collagens in BMs from diabetic patients was higher than normal. Biomechanical measurements of vascular BM flat mounts using AFM showed that their outer surface was softer than normal.