Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study.

BACKGROUND: The use of archived formalin-fixed paraffin-embedded (FFPE) tumor tissues has become a common practice in clinical and epidemiologic genetic research. Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging. Here we report our results and lessons learned from processing FFPE breast tumor tissues for a large epidemiologic study. METHODS: Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues. The yield was quantified using Qubit and fragmentation analysis by Agilent Bioanalyzer. A subset of the DNA samples were used for genome-wide DNA methylation assays and RNA samples for sequencing. The QC metrices and performance of the assays were analyzed with pre-analytical variables. RESULTS: A total of 1859 FFPE breast tumor tissues were processed. We found it critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA. Tissue punches taken from tumor-enriched regions provided the most reliable output. A median of 1475 ng DNA and 1786 ng RNA per sample was generated. The median DNA integrity number (DIN) was 3.8 and median DV200 for RNA was 33.2. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by qPCR and 92% generated data deemed high quality. Of the 130 RNA samples with DV200 ≥ 20% used in RNA-sequencing, all but 5 generated usable transcriptomic data with a mapping rate ≥ 60%. CONCLUSIONS: Dual DNA/RNA purification using Qiagen AllPrep FFPE extraction protocol is feasible for clinical and epidemiologic studies. We recommend tissue punches as a reliable source material and fine tuning of proteinase K digestion time based on tissue volume. IMPACT: Our protocol and recommendations may be adapted by future studies for successful extraction of archived tumor tissues.

Gene expression of adipokines and adipokine receptors in the tumor microenvironment: associations of lower expression with more aggressive breast tumor features.

PURPOSE: Limited epidemiologic data are available on the expression of adipokines leptin (LEP) and adiponectin (ADIPOQ) and adipokine receptors (LEPR, ADIPOR1, ADIPOR2) in the breast tumor microenvironment (TME). The associations of gene expression of these biomarkers with tumor clinicopathology are not well understood. METHODS: NanoString multiplexed assays were used to assess the gene expression levels of LEP, LEPR, ADIPOQ, ADIPOR1, and ADIPOR2 within tumor tissues among 162 Black and 55 White women with newly diagnosed breast cancer. Multivariate mixed effects models were used to estimate associations of gene expression with breast tumor clinicopathology (overall and separately among Blacks). RESULTS: Black race was associated with lower gene expression of LEPR (P = 0.002) and ADIPOR1 (P = 0.01). Lower LEP, LEPR, and ADIPOQ gene expression were associated with higher tumor grade (P = 0.0007, P < 0.0001, and P < 0.0001, respectively) and larger tumor size (P < 0.0001, P = 0.0005, and P < 0.0001, respectively). Lower ADIPOQ expression was associated with ER- status (P = 0.0005), and HER2-enriched (HER2-E; P = 0.0003) and triple-negative (TN; P = 0.002) subtypes. Lower ADIPOR2 expression was associated with Ki67+ status (P = 0.0002), ER- status (P < 0.0001), PR- status (P < 0.0001), and TN subtype (P = 0.0002). Associations of lower adipokine and adipokine receptor gene expression with ER-, HER2-E, and TN subtypes were confirmed using data from The Cancer Genome Atlas (P-values < 0.005). CONCLUSION: These findings suggest that lower expression of ADIPOQ, ADIPOR2, LEP, and LEPR in the breast TME might be indicators of more aggressive breast cancer phenotypes. Validation of these findings are warranted to elucidate the role of the adipokines and adipokine receptors in long-term breast cancer prognosis.

Blocked transcription through KvDMR1 results in absence of methylation and gene silencing resembling Beckwith-Wiedemann syndrome.

The maternally methylated KvDMR1 ICR regulates imprinted expression of a cluster of maternally expressed genes on human chromosome 11p15.5. Disruption of imprinting leads to Beckwith-Wiedemann syndrome (BWS), an overgrowth and cancer predisposition condition. In the majority of individuals with BWS, maternal-specific methylation at KvDMR1 is absent and genes under its control are repressed. We analyzed a mouse model carrying a poly(A) truncation cassette inserted to prevent RNA transcripts from elongation through KvDMR1. Maternal inheritance of this mutation resulted in absence of DNA methylation at KvDMR1, which led to biallelic expression of Kcnq1ot1 and suppression of maternally expressed genes. This study provides further evidence that transcription is required for establishment of methylation at maternal gametic DMRs. More importantly, this mouse model recapitulates the molecular phenotypic characteristics of the most common form of BWS, including loss of methylation at KvDMR1 and biallelic repression of Cdkn1c, suggesting that deficiency of maternal transcription through KvDMR1 may be an underlying cause of some BWS cases.

Surface Diffusion of Dendronized Polymers Correlates with Their Transfection Potential.

Successful intracellular delivery of therapeutics requires interactions at several liquid-solid interfaces, including cell surface, endosomal membranes, and-depending on the therapeutic-the nuclear membrane. Understanding the dynamics of polymer kinetics at the liquid-solid interface is fundamental for the design of polymers for such biomedical delivery applications. However, the effect of polymer architecture and charge density on polymer kinetics is not readily investigated using routine techniques, and the role of such parameters in the context of gene delivery remains unknown. We adopted a synthetic strategy which enabled the systematic manipulation of charge density, flexibility, and molecular weight using a dendronized linear polymeric architecture. High-speed atomic force microscopy (HS-AFM) was used as a label-free method to directly observe the polymers' dynamic properties, such as velocity, displacement, and diffusion, in physiologically relevant conditions. Importantly, we found that the physical parameters measured by HS-AFM relate to the transfection potential of the individual polymers and may be a valuable tool in screening structural polymer variants.

Nanoscale piezoelectric effect of biodegradable PLA-based composite fibers by piezoresponse force microscopy.

The piezoelectricity of the biocompatible and biodegradable polymer polylactic acid (PLA) was investigated as a potential magnetoelectric (ME) nanocomposite for biomedical applications. A key focus was to quantify the piezoelectric properties of single PLA fibers while tuning their polymer degradability through the addition of faster degrading polymer, poly (DL-lactide-co-glycolide) (PLGA), which is not a piezoelectric polymer. Piezoresponse Force Microscopy (PFM) showed that electrospun PLA fibers gave a piezoelectric response of 186 ± 28 pm. For comparison both PLA/PLGA (75/25) and PLA/PLGA (50/50) fibers gave significantly lower piezoelectric responses of 89 ± 12 pm and 50 ± 9.1 pm, respectively. For the highest content PLGA fibers, PLA/PLGA (25/75), only very few fibers exhibited a low response of 28 pm while most showed no response. Overall, an increasing PLGA content caused a decrease in the piezoelectric response, thus an expected trade-off existed between the biodegradability (i.e. PLA to PLGA content ratio) versus piezoelectricity. The findings were considered significant due to the existence of piezoelectricity in a tuneable biodegradable material that has potential to impart piezoelectric induced effects on biointeractions with the surrounding biological environment or drug interactions with the polymer to control the rate of drug release. In such applications, there is an opportunity to magnetically control the piezoelectricity and henceforth PLA/CoFe2O4 ME nanocomposite fibers with 5% and 10% of CoFe2O4 nanoparticles were also investigated. Both 5% and 10% PLA/CoFe2O4 nanocomposites gave lower piezoelectric responses compared to the PLA presumably due to the disturbance of polymer chains and dipole moments by the magnetic nanoparticles, in addition to effects from the possible inhomogeneous distribution of CoFe2O4 nanoparticles.

Single-Molecular Heteroamyloidosis of Human Islet Amyloid Polypeptide.

Human amyloids and plaques uncovered post mortem are highly heterogeneous in structure and composition, yet literature concerning the heteroaggregation of amyloid proteins is extremely scarce. This knowledge deficiency is further exacerbated by the fact that peptide delivery is a major therapeutic strategy for targeting their full-length counterparts associated with the pathologies of a range of human diseases, including dementia and type 2 diabetes (T2D). Accordingly, here we examined the coaggregation of full-length human islet amyloid polypeptide (IAPP), a peptide associated with type 2 diabetes, with its primary and secondary amyloidogenic fragments 19-29 S20G and 8-20. Single-molecular aggregation dynamics was obtained by high-speed atomic force microscopy, augmented by transmission electron microscopy, X-ray diffraction, and super-resolution stimulated emission depletion microscopy. The coaggregation significantly prolonged the pause phase of fibril elongation, increasing its dwell time by 3-fold. Surprisingly, unidirectional elongation of mature fibrils, instead of protofilaments, was observed for the coaggregation, indicating a new form of tertiary protein aggregation unknown to existing theoretical models. Further in vivo zebrafish embryonic assay indicated improved survival and hatching, as well as decreased frequency and severity of developmental abnormalities for embryos treated with the heteroaggregates of IAPP with 19-29 S20G, but not with 8-20, compared to the control, indicating the therapeutic potential of 19-29 S20G against T2D.

Differences in microRNA expression in breast cancer between women of African and European ancestry.

Breast cancer is a heterogeneous disease, characterized by molecularly and phenotypically distinct tumor subtypes, linked to disparate clinical outcomes. American women of African ancestry (AA) are more likely than those of European ancestry (EA) to be diagnosed with aggressive, estrogen receptor negative (ER-) or triple negative breast cancer, and to die of this disease. However, the underlying causes of AA predisposition to ER-/triple negative breast cancer are still largely unknown. In this study, we performed high-throughput whole-genome miRNA expression profiling in breast tissue samples from both AA and EA women. A number of differentially expressed miRNAs, i.e., DEmiRs defined as >2-fold change in expression and false discovery rate <0.05, were identified as up- or downregulated by tumor ER status or by ancestry. We found that among 102 ER-subtype-related DEmiRs identified in breast tumors, the majority of these DEmiRs were race specific, with only 23 DEmiRs shared in tumors from both AAs and EAs; this finding indicates that there are unique subsets of miRNAs differentially expressed between ER- and ER positive tumors within AAs versus EAs. Our overall results support the notion that miRNA expression patterns may differ not only by tumor subtype but by ancestry, indicating differences in tumor biology and heterogeneity of breast cancer between AAs and EAs. These results will provide the basis for further functional analysis to elucidate biological differences between AAs and EAs and to help develop targeted treatment strategies to reduce disparities in breast cancer.

Zwitterion Functionalized Silica Nanoparticle Coatings: The Effect of Particle Size on Protein, Bacteria, and Fungal Spore Adhesion.

The negative impacts that arise from biological fouling of surfaces have driven the development of coatings with unique physical and chemical properties that are able to prevent interactions with fouling species. Here, we report on low-fouling hydrophilic coatings presenting nanoscaled features prepared from different size silica nanoparticles (SiNPs) functionalized with zwitterionic chemistries. Zwitterionic sulfobetaine siloxane (SB) was reacted to SiNPs ranging in size from 7 to 75 nm. Particle stability and grafting density were confirmed using dynamic light scattering and thermogravimetric analysis. Thin coatings of nanoparticles were prepared by spin-coating aqueous particle suspensions. The resulting coatings were characterized using scanning electron microscopy, atomic force microscopy, and contact angle goniometry. SB functionalized particle coatings displayed increased hydrophilicity compared to unmodified particle coating controls while increasing particle size correlated with increased coating roughness and increased surface area. Coatings of zwitterated particles demonstrated a high degree of nonspecific protein resistance, as measured by quartz crystal microgravimetry. Adsorption of bovine serum albumin and hydrophobin proteins were reduced by up to 91 and 94%, respectively. Adhesion of bacteria ( Escherichia coli) to zwitterion modified particle coatings were also significantly reduced over both short and long-term assays. Maximum reductions of 97% and 94% were achieved over 2 and 24 h assay periods, respectively. For unmodified particle coatings, protein adsorption and bacterial adhesion were generally reduced with increasing particle size. Adhesion of fungal spores to SB modified SiNP coatings was also reduced, however no clear trends in relation to particle size were demonstrated.

Patterning and process parameter effects in 3D suspension near-field electrospinning of nanoarrays.

The extracellular matrix (ECM) contains nanofibrous proteins and proteoglycans. Nanofabrication methods have received growing interest in recent years as a means of recapitulating these elements within the ECM. Near-field electrospinning (NFES) is a versatile fibre deposition method, capable of layer-by-layer nano-fabrication. The maximum layer height is generally limited in layer-by-layer NFES as a consequence of electrostatic effects of the polymer at the surface, due to residual charge and polymer dielectric properties. This restricts the total volume achievable by layer-by-layer techniques. Surpassing this restriction presents a complex challenge, leading to research innovations aimed at increasing patterning precision, and achieving a translation from 2D to 3D additive nanofabrication. Here we investigated a means of achieving this translation through the use of 3D electrode substrates. This was addressed by in-house developed technology in which selective laser melt manufactured standing pillar electrodes were combined with a direct suspension near-field electrospinning (SNFES) technique, which implements an automated platform to manoeuvre the pillar electrodes around the emitter in order to suspend fibres in the free space between the electrode support structures. In this study SNFES was used in multiple operation modes, investigating the effects of varying process parameters, as well as pattern variations on the suspended nanoarrays. Image analysis of the nanoarrays allowed for the assessment of fibre directionality, isotropy, and diameter; identifying optimal settings to generate fibres for tissue engineering applications.

A direct 3D suspension near-field electrospinning technique for the fabrication of polymer nanoarrays.

Near-field electrospinning (NFES) is widely recognized as a versatile nanofabrication method, one suitable for applications in tissue engineering. Rapid developments in this field have given rise to layered nanofibrous scaffolds. However, this electrostatic fabrication process is limited by the electric field inhibitory effects of polymer deposition. This leads to a major challenge: how to surpass this limitation on planar/layered constructs. While the current focus in this area largely lies with the investigation of new materials, techniques and increasing precision of NFES systems and patterning, exploration of complex collector substrates is often restricted by (i) available technology and (ii) access to complex electrode manufacturing tools. To achieve nanofiber arrays suspended in free space, this paper documents both the development of an integrated NFES system and the potential of standing electrodes manufactured via selective laser melting. This system was first tested by 2D patterning on planar silicon, using polyethylene oxide polymer solution. To demonstrate suspension NFES, two patterns operating within and around the standing electrodes produced high volume suspended nanoarrays. Image analysis of the arrays allowed for the assessment of fiber directionality and isotropy. By scanning electron microscopy, it was found that a mean fiber diameter of 310 nm of the arrays was achieved. Effectively manoeuvring between the electrode pillars required a precision automated system (unavailable off-the-shelf), developed in-house. This technique can be applied to the fabrication of nanofiber structures of sufficient volume for tissue engineering.

Improving massive experiments with threshold blocking.

Inferences from randomized experiments can be improved by blocking: assigning treatment in fixed proportions within groups of similar units. However, the use of the method is limited by the difficulty in deriving these groups. Current blocking methods are restricted to special cases or run in exponential time; are not sensitive to clustering of data points; and are often heuristic, providing an unsatisfactory solution in many common instances. We present an algorithm that implements a widely applicable class of blocking-threshold blocking-that solves these problems. Given a minimum required group size and a distance metric, we study the blocking problem of minimizing the maximum distance between any two units within the same group. We prove this is a nondeterministic polynomial-time hard problem and derive an approximation algorithm that yields a blocking where the maximum distance is guaranteed to be, at most, four times the optimal value. This algorithm runs in O(n log n) time with O(n) space complexity. This makes it, to our knowledge, the first blocking method with an ensured level of performance that works in massive experiments. Whereas many commonly used algorithms form pairs of units, our algorithm constructs the groups flexibly for any chosen minimum size. This facilitates complex experiments with several treatment arms and clustered data. A simulation study demonstrates the efficiency and efficacy of the algorithm; tens of millions of units can be blocked using a desktop computer in a few minutes.

Paternal allelic mutation at the Kcnq1 locus reduces pancreatic ß-cell mass by epigenetic modification of Cdkn1c.

Genetic factors are important determinants of the onset and progression of diabetes mellitus. Numerous susceptibility genes for type 2 diabetes, including potassium voltage-gated channel, KQT-like subfamily Q, member1 (KCNQ1), have been identified in humans by genome-wide analyses and other studies. Experiments with genetically modified mice have also implicated various genes in the pathogenesis of diabetes. However, the possible effects of the parent of origin for diabetes susceptibility alleles on disease onset have remained unclear. Here, we show that a mutation at the Kcnq1 locus reduces pancreatic ß-cell mass in mice by epigenetic modulation only when it is inherited from the father. The noncoding RNA KCNQ1 overlapping transcript1 (Kcnq1ot1) is expressed from the Kcnq1 locus and regulates the expression of neighboring genes on the paternal allele. We found that disruption of Kcnq1 results in reduced Kcnq1ot1 expression as well as the increased expression of cyclin-dependent kinase inhibitor 1C (Cdkn1c), an imprinted gene that encodes a cell cycle inhibitor, only when the mutation is on the paternal allele. Furthermore, histone modification at the Cdkn1c promoter region in pancreatic islets was found to contribute to this phenomenon. Our observations suggest that the Kcnq1 genomic region directly regulates pancreatic ß-cell mass and that genomic imprinting may be a determinant of the onset of diabetes mellitus.

FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?

BACKGROUND: Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions. METHODS: Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women's Circle of Health Study (WCHS). We combined 450K profiles with RNA-seq data and prioritized genes based on differential methylation by race, correlation between methylation and gene expression, and biological function. We measured tumor protein expression and assessed its relationship to DNA methylation. We evaluated associations between reproductive characteristics and DNA methylation using linear regression. RESULTS: 410 loci were differentially methylated by race, with the majority unique to ER- tumors. FOXA1 was hypermethylated in tumors from AA versus EA women with ER- cancer, and increased DNA methylation correlated with reduced RNA and protein expression. Importantly, parity was positively associated with FOXA1 methylation among AA women with ER- tumors (P = 0.022), as was number of births (P = 0.026), particularly among those who did not breastfeed (P = 0.008). These same relationships were not observed among EA women, although statistical power was more limited. CONCLUSIONS: Methylation and expression of FOXA1 is likely impacted by parity and breastfeeding. Because FOXA1 regulates a luminal gene expression signature in progenitor cells and represses the basal phenotype, this could be a mechanism that links these reproductive exposures with ER- breast cancer.

Electro-mechano responsive properties of gelatin methacrylate (GelMA) hydrogel on conducting polymer electrodes quantified using atomic force microscopy.

Electrical stimulation of hydrogels has been performed to enable micro-actuation or controlled movement of ions and biomolecules such as in drug release applications. Hydrogels are also increasingly used as low modulus, biocompatible coatings on electrode devices and thus are exposed to the effects of electrical stimulation. As such, there is growing interest in the latter, especially on the dynamic and nanoscale physical properties of hydrogels. Here, we report on the electro-mechano properties of photocrosslinkable gelatin methacrylate (GelMA) hydrogel applied as coatings on conducting polymer polypyrrole-dodecylbenze sulfonate (PPy-DBSA) electrodes. In particular, Electrochemical-Atomic Force Microscopy (EC-AFM) was used to quantify the nanoscale actuation and dynamic changes in Young's modulus as the GelMA coating was electrically stimulated via the underlying PPy-DBSA electrode. Pulsed electrical stimulation was shown to induce dynamic expansion and contraction, or nanoscale actuation, of the GelMA hydrogel due to the reversible ingress of electrolyte ions and associated changes in osmotic pressure during oxidation and reduction of the PPy-DBSA film. In addition, dynamic changes in the Young's modulus of up to 50% were observed in the hydrogel and correlated with the actuation process and ion diffusion during oxidation and reduction of the underlying PPy-DBSA film. These dynamic properties were investigated for hydrogels with varying degrees of cross-linking, porosity and modulus, the latter ranging from ≈0.2-1 kPa. The study demonstrates an AFM-based approach to quantify the dynamic physical properties of hydrogels, which are shown to be modulated via electrical stimulation. This can enable a better understanding of the electro-mechano mechanisms that are important for the controlled release of drugs or controlling cell interactions at the hydrogel-cell interface.

Local probing of magnetoelectric properties of PVDF/Fe3O4 electrospun nanofibers by piezoresponse force microscopy.

The coupling of magnetic and electric properties in polymer-based magnetoelectric composites offers new opportunities to develop contactless electrodes, effectively without electrical connections, for less-invasive integration into devices such as energy harvesters, sensors, wearable and implantable electrodes. Understanding the macroscale-to-nanoscale conversion of the properties is important, as nanostructured and nanoscale magnetoelectric structures are increasingly fabricated. However, whilst the magnetoelectric effect at the macroscale is well established both theoretically and experimentally, it remains unclear how this effect translates to the nanoscale, or vice versa. Here, PVDF/Fe3O4 polymer-based composite nanofibers are fabricated using electrospinning to investigate their piezoelectric and magnetoelectric properties at the single nanofiber level.

Quantifying fibronectin adhesion with nanoscale spatial resolution on glycosaminoglycan doped polypyrrole using Atomic Force Microscopy.

BACKGROUND: The interaction of ECM proteins is critical in determining the performance of materials used in biomedical applications such as tissue regeneration, implantable bionics and biosensing. METHODS: To improve our understanding of ECM protein-conducting polymer interactions, we have used Atomic Force Microscopy (AFM) to elucidate the interactions of fibronectin (FN) on polypyrrole (PPy) doped with different glycosaminoglycans. RESULTS: We were able to classify four main types of FN interactions, including those related to 1) non-specific adhesion, 2) protein unfolding and subsequent unbinding from the surface, 3) desorption and 4) interactions with no adhesion. FN adhesion on PPy/hyaluronic acid showed a significantly lower density of surface adhesion with the adhesion restricted to nodule structures, as opposed to their peripheries, of the polymer morphology. In contrast, PPy/chondroitin sulfate showed a significantly higher density of surface adhesion to the point where the distribution of adhesion effectively masked the topography. Through conductive AFM imaging, we found that the conductive regions correlated with regions of FN adhesion. CONCLUSIONS: Given that the conductivity requires doping of the polymer, these findings suggest that FN adhesion is mediated by interactions with chondroitin sulfate and hyaluronic acid at the polymer surface and may be indicative of specific interactions due to contributions from electrostatic attraction between the FN and sulfate/anionic groups of the dopants. GENERAL SIGNIFICANCE: This study demonstrates the ability of AFM to resolve the protein-conducting polymer interactions at the molecular and nanoscale level, which will be important for interfacing these polymer materials with biological systems. This article is part of a Special Issue entitled Organic Bioelectronics - Novel Applications in Biomedicine.

Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells.

To understand the complex regulation of genomic imprinting it is important to determine how early embryos establish imprinted gene expression across large chromosomal domains. Long non-coding RNAs (ncRNAs) have been associated with the regulation of imprinting domains, yet their function remains undefined. Here, we investigated the mouse Kcnq1ot1 ncRNA and its role in imprinted gene regulation during preimplantation development by utilizing mouse embryonic and extra-embryonic stem cell models. Our findings demonstrate that the Kcnq1ot1 ncRNA extends 471 kb from the transcription start site. This is significant as it raises the possibility that transcription through downstream genes might play a role in their silencing, including Th, which we demonstrate possesses maternal-specific expression during early development. To distinguish between a functional role for the transcript and properties inherent to transcription of long ncRNAs, we employed RNA interference-based technology to deplete Kcnq1ot1 transcripts. We hypothesized that post-transcriptional depletion of Kcnq1ot1 ncRNA would lead to activation of normally maternal-specific protein-coding genes on the paternal chromosome. Post-transcriptional short hairpin RNA-mediated depletion in embryonic stem, trophoblast stem and extra-embryonic endoderm stem cells had no observable effect on the imprinted expression of genes within the domain, or on Kcnq1ot1 imprinting center DNA methylation, although a significant decrease in Kcnq1ot1 RNA signal volume in the nucleus was observed. These data support the argument that it is the act of transcription that plays a role in imprint maintenance during early development rather than a post-transcriptional role for the RNA itself.

Ink-on-probe hydrodynamics in atomic force microscope deposition of liquid inks.

The controlled deposition of attolitre volumes of liquids may engender novel applications such as soft, nano-tailored cell-material interfaces, multi-plexed nano-arrays for high throughput screening of biomolecular interactions, and localized delivery of reagents to reactions confined at the nano-scale. Although the deposition of small organic molecules from an AFM tip, known as dip-pen nanolithography (DPN), is being continually refined, AFM deposition of liquid inks is not well understood, and is often fraught with inconsistent deposition rates. In this work, the variation in feature-size over long term printing experiments for four model inks of varying viscosity is examined. A hierarchy of recurring phenomena is uncovered and there are attributed to ink movement and reorganisation along the cantilever itself. Simple analytical approaches to model these effects, as well as a method to gauge the degree of ink loading using the cantilever resonance frequency, are described. In light of the conclusions, the various parameters which need to be controlled in order to achieve uniform printing are dicussed. This work has implications for the nanopatterning of viscous liquids and hydrogels, encompassing ink development, the design of probes and printing protocols.

Liquid ink deposition from an atomic force microscope tip: deposition monitoring and control of feature size.

The controlled deposition of attoliter volumes of liquid inks may engender novel applications such as targeted drug delivery to single cells and localized delivery of chemical reagents at nanoscale dimensions. Although the deposition of small organic molecules from an atomic force microscope tip, known as dip-pen nanolithography (DPN), has been extensively studied, the deposition of liquid inks is little understood. In this work, we have used a set of model ink-substrate systems to develop an understanding of the deposition of viscous liquids using an unmodified AFM tip. First, the growth of dot size with increasing dwell time is characterized. The dynamics of deposition are found to vary for different ink-substrate systems, and the change in deposition rate over the course of an experiment limits our ability to quantify the ink-transfer dynamics in terms of liquid properties and substrate wettability. We find that the most critical parameter affecting the deposition rate is the volume of ink on the cantilever, an effect resulting in a 10-fold decrease in deposition rate (aL/s) over 2 h of printing time. We suggest that a driving force for deposition arises from the gradient in Laplace pressure set up when the tip touches the substrate. Second, the forces acting upon the AFM cantilever during ink deposition were measured in order to gain insight into the underlying ink-transfer mechanism. The force curve data and simple geometrical arguments were used to elucidate the shape of the ink meniscus at the instant of deposition, a methodology that may be used as an accurate and real-time means of monitoring the volume of deposited dots. Taken together, our results illustrate that liquid deposition involves a very different transfer mechanism than traditionally ascribed to DPN molecular transport.

Cell Adhesion, Elasticity, and Rupture Forces Guide Microbial Cell Death on Nanostructured Antimicrobial Titanium Surfaces.

Naturally occurring and synthetic nanostructured surfaces have been widely reported to resist microbial colonization. The majority of these studies have shown that both bacterial and fungal cells are killed upon contact and subsequent surface adhesion to such surfaces. This occurs because the presence of high-aspect-ratio structures can initiate a self-driven mechanical rupture of microbial cells during the surface adsorption process. While this technology has received a large amount of scientific and medical interest, one important question still remains: what factors drive microbial death on the surface? In this work, the interplay between microbial-surface adhesion, cell elasticity, cell membrane rupture forces, and cell lysis at the microbial-nanostructure biointerface during adsorptive processes was assessed using a combination of live confocal laser scanning microscopy, scanning electron microscopy, in situ amplitude atomic force microscopy, and single-cell force spectroscopy. Specifically, the adsorptive behavior and nanomechanical properties of live Gram-negative (Pseudomonas aeruginosa) and Gram-positive (methicillin-resistant Staphylococcus aureus) bacterial cells, as well as the fungal species Candida albicans and Cryptococcus neoformans, were assessed on unmodified and nanostructured titanium surfaces. Unmodified titanium and titanium surfaces with nanostructures were used as model substrates for investigation. For all microbial species, cell elasticity, rupture force, maximum cell-surface adhesion force, the work of adhesion, and the cell-surface tether behavior were compared to the relative cell death observed for each surface examined. For cells with a lower elastic modulus, lower force to rupture through the cell, and higher work of adhesion, the surfaces had a higher antimicrobial activity, supporting the proposed biocidal mode of action for nanostructured surfaces. This study provides direct quantification of the differences observed in the efficacy of nanostructured antimicrobial surface as a function of microbial species indicating that a universal, antimicrobial surface architecture may be hard to achieve.