Integrating Microstructured Electrospun Scaffolds in an Open Microfluidic System for in Vitro Studies of Human Patient-Derived Primary Cells

Recent studies have suggested that microenvironmental stimuli play a significant role in regulating cellular proliferation and migration, as well as in modulating self-renewal and differentiation processes of mammary cells with stem cell (SCs) properties. Recent advances in micro/nanotechnology and biomaterial synthesis/engineering currently enable the fabrication of innovative tissue culture platforms suitable for maintenance and differentiation of SCs in vitro. Here, we report the design and fabrication of an open microfluidic device (OMD) integrating removable poly(ε-caprolactone) (PCL) based electrospun scaffolds, and we demonstrate that the OMD allows investigation of the behavior of human cells during in vitro culture in real time. Electrospun scaffolds with modified surface topography and chemistry can influence attachment, proliferation, and differentiation of mammary SCs and epigenetic mechanisms that maintain luminal cell identity as a function of specific morphological or biochemical cues imparted by tailor-made fiber post-treatments. Meanwhile, the OMD architecture allows control of cell seeding and culture conditions to collect more accurate and informative in vitro assays. In perspective, integrated systems could be tailor-made to mimic specific physiological conditions of the local microenvironment and then analyze the response from screening specific drugs for more effective diagnostics, long-term prognostics, and disease intervention in personalized medicine.

Engineered Kidney Tubules for Modeling Patient-Specific Diseases and Drug Discovery

The lack of engineering systems able to faithfully reproduce complex kidney structures in vitro has made it difficult to efficiently model kidney diseases and development. Using polydimethylsiloxane (PDMS) scaffolds and a kidney-derived cell line we developed a system to rapidly engineer custom-made 3D tubules with typical renal epithelial properties. This system was successfully employed to engineer patient-specific tubules, to model polycystic kidney disease (PKD) and test drug efficacy, and to identify a potential new pharmacological treatment. By optimizing our system we constructed functional ureteric bud (UB)-like tubules from human induced pluripotent stem cells (iPSCs), and identified a combination of growth factors that induces budding morphogenesis like embryonic kidneys do. Finally, we applied this assay to investigate budding defects in UB-like tubules derived from a patient with a PAX2 mutation. Our system enables the modeling of human kidney disease and development, drug testing and discovery, and lays the groundwork for engineering anatomically correct kidney tissues in vitro and developing personalized medicine applications.

Nanotechnology Applications in Medicine

In recent years there has been a rapid increase in nanotechnology applications to medicine in order to prevent and treat diseases in the human body. The established and future applications have the potential to dramatically change medical science. The present paper will give a few examples that could transform common medical procedures.

Plastic ingestion in aquatic-associated bird species in southern Portugal

Excessive use of plastics in daily life and the inappropriate disposal of plastic products are severely affecting wildlife species in both coastal and aquatic environments. Birds are top-predators, exposed to all threats affecting their environments, making them ideal sentinel organisms for monitoring ecosystems change. We set a baseline assessment of the prevalence of marine plastic litter affecting multi-species populations of aquatic birds in southern Portugal. By examining 160 stomach contents from 8 species of aquatic birds, we show that 22.5% were affected by plastic debris. Plastic was found in Ciconia ciconia, Larus fuscus and L. michahellis. Ciconia ciconia ingested the highest amount (number of items and total mass) of plastic debris. Polydimethylsiloxane (PDMS, silicones) was the most abundant polymer and was recorded only in C. ciconia. Plastic ingestion baseline data are of crucial importance to evaluate changes through time and among regions and to define management and conservation strategies.

Simultaneous Electro-Optical Tracking for Nanoparticle Recognition and Counting

We present the first detailed experimental observation and analysis of nanoparticle electrophoresis through a nanochannel obtained with synchronous high-bandwidth electrical and camera recordings. Optically determined particle diffusion coefficients agree with values extracted from fitting electrical transport measurements to distributions from 1D Fokker-Planck diffusion-drift theory. This combined tracking strategy enables optical recognition and electrical characterization of nanoparticles in solution, which can have a broad range of applications in biology and materials science.

Stretching of DNA confined in nanochannels with charged walls

There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.

Selective protein detection with a dsLNA-functionalized nanopore

In the last years, nanopore technology has been increasingly exploited for biomolecule detection and analysis. Recently, the main focus of the research has moved from the study of nucleic acids to the analysis of proteins and DNA-protein complexes. In this paper, chemically functionalized solid-state nanopore has been used to recognize Nuclear Factor-kappa B proteins (NF-κB), that are involved in several disorders and inflammation processes, so that their identification is of crucial importance for prognostic applications. In particular, we show that it is possible to electrically detect the specific interaction between p50, a protein belonging to the NF-κB family, and dsLNA probe molecules covalently attached to the surface of a FIB fabricated SiN pore. The obtained results have been compared with those related to BSA protein, which does not interact with the used probes. Finally, the potential of the device has been further tested by analyzing a whole cell extract. In this case, three principal peaks in the distribution of electrical event duration can be identified, corresponding to different interacting NF-κB complexes, so that the methodology appears to be effective also to study biological samples of considerable complexity. Ultimately, the presented data emphasize the selectivity and versatility of the functionalized nanopore device, demonstrating its applicability in bioanalytics and advanced diagnostics.

Size and functional tuning of solid state nanopores by chemical functionalization

We demonstrate the possibility of using a simple functionalization procedure, based on an initial vapour-phase silanization, to control the size and functionality of solid state nanopores. The presented results show that, by varying the silanization time, it is possible to modify the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing a specific sensing selectivity. The proposed method allows us to tune the nanopore biosensor adapting it to the specific final application, and it can be efficiently applied when the pore initial diameter does not exceed a limit dimension related to the mean free path of the silane molecules at the working pressure.

Label-free, atomic force microscopy-based mapping of DNA intrinsic curvature for the nanoscale comparative analysis of bent duplexes

We propose a method for the characterization of the local intrinsic curvature of adsorbed DNA molecules. It relies on a novel statistical chain descriptor, namely the ensemble averaged product of curvatures for two nanosized segments, symmetrically placed on the contour of atomic force microscopy imaged chains. We demonstrate by theoretical arguments and experimental investigation of representative samples that the fine mapping of the average product along the molecular backbone generates a characteristic pattern of variation that effectively highlights all pairs of DNA tracts with large intrinsic curvature. The centrosymmetric character of the chain descriptor enables targetting strands with unknown orientation. This overcomes a remarkable limitation of the current experimental strategies that estimate curvature maps solely from the trajectories of end-labeled molecules or palindromes. As a consequence our approach paves the way for a reliable, unbiased, label-free comparative analysis of bent duplexes, aimed to detect local conformational changes of physical or biological relevance in large sample numbers. Notably, such an assay is virtually inaccessible to the automated intrinsic curvature computation algorithms proposed so far. We foresee several challenging applications, including the validation of DNA adsorption and bending models by experiments and the discrimination of specimens for genetic screening purposes.

Order versus Disorder: in vivo bone formation within osteoconductive scaffolds

In modern biomaterial design the generation of an environment mimicking some of the extracellular matrix features is envisaged to support molecular cross-talk between cells and scaffolds during tissue formation/remodeling. In bone substitutes chemical biomimesis has been particularly exploited; conversely, the relevance of pre-determined scaffold architecture for regenerated bone outputs is still unclear. Thus we aimed to demonstrate that a different organization of collagen fibers within newly formed bone under unloading conditions can be generated by differently architectured scaffolds. An ordered and confined geometry of hydroxyapatite foams concentrated collagen fibers within the pores, and triggered their self-assembly in a cholesteric-banded pattern, resulting in compact lamellar bone. Conversely, when progenitor cells were loaded onto nanofibrous collagen-based sponges, new collagen fibers were distributed in a nematic phase, resulting mostly in woven isotropic bone. Thus specific biomaterial design relevantly contributes to properly drive collagen fibers assembly to target bone regeneration.

DNA detection with a polymeric nanochannel device

We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.

"DNA-Dressed NAnopore" for complementary sequence detection

Single molecule electrical sensing with nanopores is a rapidly developing field with potential revolutionary effects on bioanalytics and diagnostics. The recent success of this technology is in the simplicity of its working principle, which exploits the conductance modulations induced by the electrophoretic translocation of molecules through a nanometric channel. Initially proposed as fast and powerful tools for molecular stochastic sensing, nanopores find now application in a range of different domains, thanks to the possibility of finely tuning their surface properties, thus introducing artificial binding and recognition sites. Here we show the results of DNA translocation and hybridization experiments at the single molecule level by a novel class of selective biosensor devices that we call "DNA-Dressed NAnopore" (DNA(2)), based on solid state nanopore with large initial dimensions, resized and activated by functionalization with DNA molecules. The presented data demonstrate the ability of the DNA(2) to selectively detect complementary target sequences, that is to distinguish between molecules depending on their affinity to the functionalization. The DNA(2) can thus constitute the basis for the design of integrable parallel devices for mutation DNA analysis, diagnostics and bioanalytic investigations.

DNA manipulation with elastomeric nanostructures fabricated by soft-moulding of a FIB-patterned stamp

A Focused Ion Beam (FIB)-patterned silicon mould is used to fabricate elastomeric nanostructures, whose cross-section can be dynamically and reversibly tuned by applying a controlled mechanical stress. Direct-write, based on FIB milling, allows the fabrication of nanostructures with a variety of different geometries, aspect ratio, spacing and distribution offering a higher flexibility compared to other nanopatterning approaches. Moreover, a simple double replication process based on poly(dimethylsiloxane) permits a strong reduction of the fabrication costs that makes this approach well-suited for the production of low cost nanofluidic devices. DNA stretching and single molecule manipulation capabilities of these platforms have been successfully demonstrated.

Binding force measurement of NF-κB-ODNs interaction: an AFM based decoy and drug testing tool

Interaction between transcription factors and DNA are essential for regulating gene transcription. The Nuclear factor-κB (NF-κB) is a ubiquitous transcription factor involved in cell signalling and its failure is a principal cause of several autoimmune and auto-inflammatory disorders. In this paper we have developed an atomic force microscopy (AFM) method to quantitatively characterise the interaction force between NF-κB and DNA or LNA (locked nucleic acid) double strand molecules containing the NF responsive elements (RE). This process allows the simple testing and selection of LNA based decoy molecules to be used in NF-κB modulation decoy strategies. Furthermore the proposed methodology is also suitable for testing drug efficacy on the modulation of NF-κB binding to its nucleic acid target sequence. A biological AFM based sensor is therefore considered appropriate for characterising transcription factors and selecting molecules to modulate their activity.

Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing

We present data concerning the electrical properties of a class of biosensor devices based on bio-functionalized solid state nanopores able to detect different kinds of interactions between probe molecules, chemically attached to the pore surface, and target molecules present in solution and electrophoretically drawn through the nanometric channel. The great potentiality of this approach resides in the fact that the functionalization of a quite large pore (up to 50-60 nm) allows a sufficient diameter reduction for the attainment of a single molecule sensing dimension and selective activation, without the need for further material deposition, such as metal or oxides, or localized surface modification. The results indicate that it will be possible, in the near future, to conceive and design devices for parallel analysis of biological samples made of arrays of nanopores differently functionalized, fabricated by standard lithographic techniques, with important applications in the field of molecular diagnosis.

Nanofriction of neon films on superconducting lead

With a quartz crystal microbalance technique we have studied the nanofriction of neon monolayers deposited on a lead surface at a temperature around 7 K. Unlike heavier adsorbates, Ne is found to systematically slide at such low temperatures without any evidence of pinning. The crossing of the Pb superconducting-metal transition is not accompanied by any change in dissipation, suggesting that the electronic contribution to friction is negligible for this system.

DNA-functionalized solid state nanopore for biosensing

The possible use of nanopores for single DNA molecules biosensing has been demonstrated, but much remains to do in order to develop advanced engineered devices with enhanced stability, and controlled geometry and surface properties. Here we present morphological and electrical characterization of solid state silicon nitride nanopores fabricated by focused ion beam direct milling and chemically functionalized by probe oligonucleotides, with the final aim of developing a versatile tool for biosensing and gene expression profiling.

Applications of metal surfaces nanostructured by ion beam sputtering

We review results relative to the formation of regular nanoscale patterns on metal substrates exposed to defocused ion beam irradiation. Particular emphasis is placed on work which demonstrates the possibility of controllably modifying chemico-physical properties of the material by tailoring the nanoscale morphology during IBS patterning. Starting from the well-established results found on single-crystal model systems, we show how the controlled modification of the atomic step termination can deeply affect chemical reactivity or magnetic anisotropy. We then look in greater detail at the more recent attempts focused on the extension of IBS patterning on supported polycrystalline metal films, a promising class of systems in view of potential applications. A modification of the functional properties of metal films can also be obtained by forcing a shape anisotropy of the nanostructures. The modification of the optical response of polycrystalline metal nanowires supported on anisotropic templates produced by IBS provides a clear example of this.

Deformation and adhesion of elastomer poly(dimethylsiloxane) colloidal AFM probes

We report on the synthesis and characterization of elastomer colloidal AFM probes. Poly(dimethylsiloxane) microparticles, obtained by water emulsification and cross-linking of viscous prepolymers, are glued to AFM cantilevers and used for contact mechanics investigations on smooth substrates: in detail cyclic loading-unloading experiments are carried on ion-sputtered mica, the deformation rate and dwell time being separately controlled. We analyze load-penetration curves and pull-off forces with models due respectively to Zener; Maugis and Barquins; and Greenwood and Johnson and account for bulk creep, interfacial viscoelasticity, and structural rearrangements at the polymer-substrate interface. A good agreement is found between experiments and theory, with a straightforward estimation of colloidal probes' material parameters. We suggest the use of such probes for novel contact mechanics experiments involving fully reversible deformations at the submicrometer scale.

Friction laws for lubricated nanocontacts

We have used friction force microscopy to probe friction laws for nanoasperities sliding on atomically flat substrates under controlled atmosphere and liquid environment, respectively. A power law relates friction force and normal load in dry air, whereas a linear relationship, i.e., Amontons' law, is observed for junctions fully immersed in model lubricants, namely, octamethylciclotetrasiloxane and squalane. Lubricated contacts display a remarkable friction reduction, with liquid and substrate specific friction coefficients. Comparison with molecular dynamics simulations suggests that load-bearing boundary layers at junction entrance cause the appearance of Amontons' law and impart atomic-scale character to the sliding process; continuum friction models are on the contrary of limited predictive power when applied to lubrication effects. An attempt is done to define general working conditions leading to the manifestation of nanoscale lubricity due to adsorbed boundary layers.

Structural depinning of Ne monolayers on Pb at T < 6/5 K

We have studied the nanofriction of Ne monolayers with a quartz-crystal microbalance technique at temperatures below 6.5 K and in ultrahigh-vacuum conditions. Very homogeneous and smooth lead electrodes have been physically deposited on a quartz blank at 150 K and then annealed at room temperatures. With such a Pb-plated quartz-crystal microbalance, we have observed a pronounced depinning transition separating a low-coverage region, where the film is nearly locked to the oscillating electrode, from a high-coverage region characterized by slippage at the solid-fluid boundary. Such a behavior has been found to be very reproducible. These data are suggestive of a structural depinning of the solid Ne film when it becomes incommensurate with the lead substrate, in agreement with the results of an extensive molecular-dynamics study.

New insights on the stereodynamics of ethylene adsorption on an oxygen-precovered silver surface

The control of spatial orientation of molecules has a great influence on the stereodynamics of elementary processes occurring both in homogeneous and heterogeneous phases. Nonpolar molecules have so far escaped direct experimental investigations because of their poor sensitivity to several external constraints. Recently, it has been shown that the collisional alignment produced in supersonic expansions coupled with molecular-beam velocity selection can help solve such problems. Here we show that the sticking probability of ethylene, a nonpolar molecule prototypical of unsaturated hydrocarbons, on an O(2)-precovered Ag(001) surface is larger for molecules approaching in a helicopter-like motion than for those cartwheeling. A mechanism involving a weakly bound precursor state is suggested, with helicopter molecules having a lower chance of being scattered back into the gas phase than cartwheels when colliding with preadsorbed ethylene.

Stereodynamic Effects in the Adsorption of Propylene Molecules on Ag(001)

We report on the experimental evidence of the role of rotational alignment of the gas-phase molecules in the interaction of propylene with Ag(001). Molecular alignment has been controlled by a velocity selection of the impinging molecules, flying in a supersonic seeded molecular beam. The experimental findings indicate that at low surface coverage the sticking probability is independent of molecular alignment, while when coverage exceeds few percent of a monolayer, molecules impinging rotating parallel to the surface (helicopter-like configuration) achieve a higher chance to be trapped than those which impinge rotating perpendicularly (cartwheels). The sudden appearance of a large stereodynamic effect suggests that the adsorption proceeds via a mobile precursor state and is tentatively correlated with a change in the configuration of the added propylene molecules, which adsorb tilted rather than flat at the surface.

Unexpected Behavior of the Surface Composition of PtRh Alloys during Chemical Reaction

The changes in the surface composition of a Pt(50)Rh(50)(100) alloy due to an ongoing 2H(2) + O(2)-->2H(2)O chemical reaction have been studied in situ. Exploiting the high-energy resolution and surface sensitivity of synchrotron radiation core-level spectroscopy it was possible to monitor the population of the two transitions metals atoms at the gas-surface interface. Sequences of fast high-resolution core-level spectra of the Rh3d(5/2), Pt4f(7/2), and O1s core levels showed a continuous exchange of atoms between the first and subsurface layers. An unexpected Pt surface enrichement was found under slightly oxidizing conditions, opposite to what found in a highly oxidizing atmosphere.

Self-organized formation of rhomboidal nanopyramids on fcc(110) metal surfaces

We report on the far from equilibrium self-organized morphologies obtained after Xe ion irradiation of the Rh(110) and Cu(110) surfaces. Here we experimentally identify by means of high resolution LEED a novel interfacial state characterized by a rhomboidal pyramid islanding with majority steps oriented along nonequilibrium low-symmetry directions. The formation of the novel rhomboidal pyramid state and the transition to the well-known rippled phases results from a delicate interplay of kinetic processes which are controlled by acting on temperature, ion flux, and impact energy.

Experimental investigation of the contact mechanics of rough fractal surfaces

The nonstationary character of roughness is a widely recognized property of surface morphology and suggests modeling several solid surfaces by fractal geometry. In the field of contact mechanics, this demands novel investigations attempting to clarify the role of multiscale roughness during physical contact. Here we review the results we recently obtained in the characterization of the contact mechanics of fractal surfaces by depth-sensing indentation. One class of experiments was conducted on organic thin films, load-displacement curves being acquired by atomic force microscopy using custom-designed tips. Another class of experiments focused on well-defined crystalline and mechanically polished ceramic substrates probed by a traditional nanoindenter. We observed the first-loading cycle to be considerably affected by surface roughness. Plastic failure was found to dominate incipient contact while contact stiffness increased on decreasing fractal dimension and roughness. Our findings suggest fractal parameters to drive contact mechanics whenever the penetration depth is kept below the interface width.

Adatom ascending at step edges and faceting on fcc metal (110) surfaces

Using first-principles total-energy calculations, we show that an adatom can easily climb up at monatomic-layer-high steps on several representative fcc metal (110) surfaces via a place exchange mechanism. Inclusion of such novel adatom ascending processes in kinetic Monte Carlo simulations of Al(110) homoepitaxy as a prototypical model system can lead to the existence of an intriguing faceting instability, whose dynamical evolution and kinetic nature are explored in comparison with experimental observations.

Uniaxial magnetic anisotropy in nanostructured Co/Cu(001): from surface ripples to nanowires

We have investigated the correlation between morphology and magnetic anisotropy in nanostructured Co films on Cu(001). The formation of nanoscale ripples by ion erosion is found to deeply affect the magnetic properties of the Co film. A surface-type uniaxial magnetic anisotropy with easy axis parallel to the ripples is observed. The origin of the magnetic anisotropy has been identified with the modification of thermodynamic-step distribution induced by ripple formation. At higher ion doses, when Co ripples detach and crystalline nanowires form, a strong enhancement of the magnetic anisotropy due to magnetostatic contributions is observed.

Nanocrystal formation and faceting instability in Al(110) homoepitaxy: true upward adatom diffusion at step edges and island corners

Using atomic force microscopy and spot-profile analyzing low energy electron diffraction, we have observed the existence of a striking faceting instability in Al(110) homoepitaxy, characterized by the formation of nanocrystals with well-defined facets. These hut-shaped nanocrystals are over tenfold higher than the total film coverage, and coexist in a bimodal growth mode with much shallower and more populous surface mounds. We further use density functional theory calculations to elucidate the microscopic origin of the faceting instability, induced by surprisingly low activation barriers for adatom ascent at step edges and island corners.

The contact mechanics of fractal surfaces

The role of surface roughness in contact mechanics is relevant to processes ranging from adhesion to friction, wear and lubrication. It also promises to have a deep impact on applied science, including coatings technology and design of microelectromechanical systems. Despite the considerable results achieved by indentation experiments, particularly in the measurement of bulk hardness on nanometre scales, the contact behaviour of realistic surfaces, showing random multiscale roughness, remains largely unknown. Here we report experimental results concerning the mechanical response of self-affine thin films indented by a micrometric flat probe. The specimens, made of cluster-assembled carbon or of sexithienyl, an organic molecular material, were chosen as prototype systems for the broad class of self-affine fractal interfaces, today including surfaces grown under non-equilibrium conditions, fractures, manufactured metal surfaces and solidified liquid fronts. We observe that a regime exists in which roughness drives the contact mechanics: in this range surface stiffness varies by a few orders of magnitude on small but significant changes of fractal parameters. As a consequence, we demonstrate that soft solid interfaces can be appreciably strengthened by reducing both fractal dimension and surface roughness. This indicates a general route for tailoring the mechanical properties of solid bodies.

Is ion sputtering always a "negative homoepitaxial deposition"?

We present a scanning tunneling microscopy study of the direct comparison between homoepitaxial deposition and surface ion sputtering on the Ag(001) system. At a temperature of 200 K, sputtering results in mound formation similar to the epitaxy case, while at higher temperatures an erosive regime sets in with the appearance of regular square pits. Contrary to the conventional wisdom, which considers ion sputtering as a deposition of vacancies, the analysis of single ion impact events reveals that the process produces both adatom and vacancy clusters. The key parameter determining the temperature dependence of surface morphology turns out to be the mobility of the adatom clusters which exceeds that of vacancy clusters.

Ripple rotation in multilayer homoepitaxy

We have investigated the homoepitaxial growth of Ag(110) in the multilayer regime. After deposition of 30 monolayers of Ag at a temperature of 210 K a ripplelike surface instability is produced and the ridges of the ripples, as well as the majority steps, are found to be parallel to <11;0> which is the thermodynamically favored orientation. As the deposition temperature is decreased to 130 K, an unexpected 90 degrees switch of the ripple orientation is observed. The ridges of the ripples and the steps are in this case parallel to <100>. In the intermediate temperature range a checkerboard of rectangular mounds results. We interpret our results in terms of the peculiar hierarchy of interlayer and intralayer diffusion barriers present on the anisotropic Ag(110) surface.