Publications by year
In Press
Cama J, Al Nahas K, Fletcher M, Hammond K, Ryadnov MG, Keyser UF, Pagliara S (In Press). An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics.
Abstract:
An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics
AbstractAntimicrobial resistance challenges the ability of modern medicine to contain infections. Given the dire need for new antimicrobials, peptide antibiotics hold particular promise. These agents hit multiple targets in bacteria starting with their most exposed regions – their membranes. However, suitable assays to quantify the efficacy of peptide antibiotics at the membrane and cellular level have been lacking. Here, we employ two complementary microfluidic platforms to probe the structure-activity relationships of two experimental series of peptide antibiotics. We reveal strong correlations between each peptide’s physicochemical activity at the membrane level and biological activity at the cellular level by assaying the membranolytic activities of the antibiotics on hundreds of individual giant lipid vesicles, and quantifying phenotypic responses within clonal bacterial populations with single-cell resolution. Our strategy proved capable of detecting differential responses for peptides with single amino acid substitutions between them, and can accelerate the rational design and development of peptide antimicrobials.
Abstract.
Cama J, Voliotis M, Metz J, Smith A, Iannucci J, Keyser UF, Tsaneva-Atanasova K, Pagliara S (In Press). Antibiotic transport kinetics in Gram-negative bacteria revealed via single-cell uptake analysis and mathematical modelling.
Abstract:
Antibiotic transport kinetics in Gram-negative bacteria revealed via single-cell uptake analysis and mathematical modelling
AbstractThe double-membrane cell envelope of Gram-negative bacteria is a formidable barrier to intracellular antibiotic accumulation. A quantitative understanding of antibiotic transport in these cells is crucial for drug development, but this has proved elusive due to the complexity of the problem and a dearth of suitable investigative techniques. Here we combine microfluidics and time-lapse auto-fluorescence microscopy to quantify antibiotic uptake label-free in hundreds of individual Escherichia coli cells. By manipulating the microenvironment, we showed that drug (ofloxacin) accumulation is higher in growing versus non-growing cells. Using genetic knockouts, we provide the first direct evidence that growth phase is more important for drug accumulation than the presence or absence of individual transport pathways. We use our experimental results to inform a mathematical model that predicts drug accumulation kinetics in subcellular compartments. These novel experimental and theoretical results pave the way for the rational design of new Gram-negative antibiotics.
Abstract.
Blaskovich MA, Phetsang W, Stone MRL, Lapinska U, Pagliara S, Bhalla R, Cooper MA (In Press). Antibiotic-derived molecular probes for bacterial imaging.
International Society for Optics and Photonics,
10863Abstract:
Antibiotic-derived molecular probes for bacterial imaging
Infections caused by drug resistant bacteria poses a significant threat to global human health, with predicted annual mortality of 10 million by 2050. While much attention is focused on developing better therapies, improving diagnosis would allow for rapid initiation of optimal treatment, reducing unnecessary antibiotic use and enhancing therapeutic outcomes. There are currently no whole body imaging techniques in clinical use that are capable of specifically identifying bacterial infections. We have developed antibiotic-derived fluorescent probes that bind and illuminate either Gram-positive or Gram-negative bacteria with high specificity and selectivity over mammalian cells. Antibiotics are functionalised with an azide substituent in a position that minimises effects on antibiotic activity. These are reacted by facile 1,3-dipolar cycloaddition with alkyne-substituted imaging components such as visible or near-infrared fluorophores. The resulting adducts can be used as tools to image bacteria in vitro and in vivo. We have successfully functionalised representatives of seven major antibiotic classes. These derivatives retain antibacterial activity, and have been coupled with a range of fluorophores. Fluorescent versions of vancomycin and polymyxin B are particularly useful for specific labelling of G+ve and G-ve bacteria, respectively. Preliminary studies have now extended the visualisation component to include moieties compatible with PET imaging.
Abstract.
Dimitriu T, Kurilovich E, Lapinska U, Severinov K, Pagliara S, Szczelkun MD, Westra ER (In Press). Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity.
Abstract:
Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity
AbstractPhage therapy can be used in combination with antibiotics to combat infections with bacterial pathogens1–3. However, bacteria can rapidly evolve phage resistance via receptor mutation, or using their CRISPR-Cas adaptive immune systems4, which insert short phage-derived sequences into CRISPR loci in the bacterial genome5 to guide sequence-specific cleavage of cognate sequences6. Unlike CRISPR-Cas immunity, mutation of the phage receptor leads to attenuated virulence when the opportunistic pathogen Pseudomonas aeruginosa is infected with its phage DMS3vir7, which underscores the need to predict how phage resistance evolves under clinically relevant conditions. Here, using eight antibiotics with various modes of action, we show that bacteriostatic antibiotics (which inhibit cell growth without killing) specifically promote evolution of CRISPR-Cas immunity in P. aeruginosa by slowing down phage development and providing more time for cells to acquire phage-derived sequences and mount an immune response. Our data show that some antimicrobial treatments can contribute to the evolution of phage-resistant pathogens with high virulence.
Abstract.
Conners R, McLaren M, Łapińska U, Sanders K, Stone MRL, Blaskovich MAT, Pagliara S, Daum B, Rakonjac J, Gold VAM, et al (In Press). CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage.
Abstract:
CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage
AbstractThe Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.
Abstract.
Łapińska U, Voliotis M, Lee KK, Campey A, Stone MRL, Phetsang W, Zhang B, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S, et al (In Press). Fast bacterial growth reduces antibiotic accumulation and efficacy.
Abstract:
Fast bacterial growth reduces antibiotic accumulation and efficacy
AbstractPhenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here we hypothesize that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations ofEscherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepaciaandStaphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast growing variants, including efflux that can reduce macrolide accumulation. Using this new knowledge, we phenotypically engineered bacterial populations by eradicating variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.
Abstract.
Binsley J, Pagliara S, Ogrin F (In Press). Numerical Investigation of Flexible Purcell-like Integrated Microfluidic Pumps.
Journal of Applied PhysicsAbstract:
Numerical Investigation of Flexible Purcell-like Integrated Microfluidic Pumps
Integrating miniature pumps within microfluidic devices is crucial for advancing point-of-care diagnostics. Understanding the emergence of flow from novel integrated pumping systems is the first step in their successful implementation. A Purcell-like elasto-magnetic integrated microfluidic pump has been simulated in COMSOL Multiphysics and its performance has been investigatedand evaluated. An elastic, cilia-like element contains an embedded magnet which allows for actuation via a weak, uniaxial, sinusoidally oscillating, external magnetic field. Pumping performance is correlated against a number of variables, such as the frequency of the driving field, and the proximity of the pump to the channel walls; in order to understand the emergence of the pumping behaviour. Crucially, these simulations capture many of the trends observed experimentally, and shed light on the key interactions. The proximity of the channel walls in the in-plane direction strongly determines the direction of net fluid flow. This characterisation has important implications for the design and optimisation of this pump in practical applications.
Abstract.
Morrish R, Yim K, Pagliara S, Palombo F, Chahwan R, Stone N (In Press). Single cell label-free probing of chromatin dynamics during B lymphocyte maturation. Frontiers in Cell and Developmental Biology
2023
Binsley JL, Myers TO, Pagliara S, Ogrin FY (2023). Herringbone micromixers for particle filtration.
Biomicrofluidics,
17(1).
Abstract:
Herringbone micromixers for particle filtration.
Herringbone micromixers are a powerful tool for introducing advection into microfluidic systems. While these mixers are typically used for mixing fluids faster than the rate of diffusion, there has been recent interest in using the device to enhance interactions between suspended particles and channel walls. We show how the common approximations applied to herringbone micromixer theory can have a significant impact on results. We show that the inclusion of gravity can greatly alter the interaction probability between suspended particles and channel walls. We also investigate the proposed impedance matching condition and the inclusion of imperfect binding using numerical methods, and investigate transient behaviors using an experimental system. These results indicate that while traditional methods, such as simple streamline analysis, remain powerful tools, it should not be considered predictive in the general case.
Abstract.
Author URL.
Zhang Y, Kepiro I, Ryadnov MG, Pagliara S (2023). Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes.
Microbiol Spectr,
11(1).
Abstract:
Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes.
With the spread of multidrug-resistant bacteria, there has been an increasing focus on molecular classes that have not yet yielded an antibiotic. A key capability for assessing and prescribing new antibacterial treatments is to compare the effects antibacterial agents have on bacterial growth at a phenotypic, single-cell level. Here, we combined time-lapse microscopy with microfluidics to investigate the concentration-dependent killing kinetics of stationary-phase Escherichia coli cells. We used antibacterial agents from three different molecular classes, β-lactams and fluoroquinolones, with the known antibiotics ampicillin and ciprofloxacin, respectively, and a new experimental class, protein Ψ-capsids. We found that bacterial cells elongated when treated with ampicillin and ciprofloxacin used at their minimum inhibitory concentration (MIC). This was in contrast to Ψ-capsids, which arrested bacterial elongation within the first two hours of treatment. At concentrations exceeding the MIC, all the antibacterial agents tested arrested bacterial growth within the first 2 h of treatment. Further, our single-cell experiments revealed differences in the modes of action of three different agents. At the MIC, ampicillin and ciprofloxacin caused the lysis of bacterial cells, whereas at higher concentrations, the mode of action shifted toward membrane disruption. The Ψ-capsids killed cells by disrupting their membranes at all concentrations tested. Finally, at increasing concentrations, ampicillin and Ψ-capsids reduced the fraction of the population that survived treatment in a viable but nonculturable state, whereas ciprofloxacin increased this fraction. This study introduces an effective capability to differentiate the killing kinetics of antibacterial agents from different molecular classes and offers a high content analysis of antibacterial mechanisms at the single-cell level. IMPORTANCE Antibiotics act against bacterial pathogens by inhibiting their growth or killing them directly. Different modes of action determine different antibacterial responses, whereas phenotypic differences in bacteria can challenge the efficacy of antibiotics. Therefore, it is important to be able to differentiate the concentration-dependent killing kinetics of antibacterial agents at a single-cell level, in particular for molecular classes which have not yielded an antibiotic before. Here, we measured single-cell responses using microfluidics-enabled imaging, revealing that a novel class of antibacterial agents, protein Ψ-capsids, arrests bacterial elongation at the onset of treatment, whereas elongation continues for cells treated with β-lactam and fluoroquinolone antibiotics. The study advances our current understanding of antibacterial function and offers an effective strategy for the comparative design of new antibacterial therapies, as well as clinical antibiotic susceptibility testing.
Abstract.
Author URL.
Zhang B, Phetsang W, Stone MRL, Kc S, Butler MS, Cooper MA, Elliott AG, Łapińska U, Voliotis M, Tsaneva-Atanasova K, et al (2023). Synthesis of vancomycin fluorescent probes that retain antimicrobial activity, identify Gram-positive bacteria, and detect Gram-negative outer membrane damage.
Commun Biol,
6(1).
Abstract:
Synthesis of vancomycin fluorescent probes that retain antimicrobial activity, identify Gram-positive bacteria, and detect Gram-negative outer membrane damage.
Antimicrobial resistance is an urgent threat to human health, and new antibacterial drugs are desperately needed, as are research tools to aid in their discovery and development. Vancomycin is a glycopeptide antibiotic that is widely used for the treatment of Gram-positive infections, such as life-threatening systemic diseases caused by methicillin-resistant Staphylococcus aureus (MRSA). Here we demonstrate that modification of vancomycin by introduction of an azide substituent provides a versatile intermediate that can undergo copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction with various alkynes to readily prepare vancomycin fluorescent probes. We describe the facile synthesis of three probes that retain similar antibacterial profiles to the parent vancomycin antibiotic. We demonstrate the versatility of these probes for the detection and visualisation of Gram-positive bacteria by a range of methods, including plate reader quantification, flow cytometry analysis, high-resolution microscopy imaging, and single cell microfluidics analysis. In parallel, we demonstrate their utility in measuring outer-membrane permeabilisation of Gram-negative bacteria. The probes are useful tools that may facilitate detection of infections and development of new antibiotics.
Abstract.
Author URL.
Łapińska U, Glover G, Kahveci Z, Irwin NAT, Milner DS, Tourte M, Albers S-V, Santoro AE, Richards TA, Pagliara S, et al (2023). Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes.
PLoS Biol,
21(4).
Abstract:
Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes.
One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been termed the lipid divide and possibly bestows different biophysical and biochemical characteristics on each cell type. Classic experiments suggest that bacterial membranes (formed from lipids extracted from Escherichia coli, for example) show permeability to key metabolites comparable to archaeal membranes (formed from lipids extracted from Halobacterium salinarum), yet systematic analyses based on direct measurements of membrane permeability are absent. Here, we develop a new approach for assessing the membrane permeability of approximately 10 μm unilamellar vesicles, consisting of an aqueous medium enclosed by a single lipid bilayer. Comparing the permeability of 18 metabolites demonstrates that diether glycerol-1-phosphate lipids with methyl branches, often the most abundant membrane lipids of sampled archaea, are permeable to a wide range of compounds useful for core metabolic networks, including amino acids, sugars, and nucleobases. Permeability is significantly lower in diester glycerol-3-phosphate lipids without methyl branches, the common building block of bacterial membranes. To identify the membrane characteristics that determine permeability, we use this experimental platform to test a variety of lipid forms bearing a diversity of intermediate characteristics. We found that increased membrane permeability is dependent on both the methyl branches on the lipid tails and the ether bond between the tails and the head group, both of which are present on the archaeal phospholipids. These permeability differences must have had profound effects on the cell physiology and proteome evolution of early prokaryotic forms. To explore this further, we compare the abundance and distribution of transmembrane transporter-encoding protein families present on genomes sampled from across the prokaryotic tree of life. These data demonstrate that archaea tend to have a reduced repertoire of transporter gene families, consistent with increased membrane permeation. These results demonstrate that the lipid divide demarcates a clear difference in permeability function with implications for understanding some of the earliest transitions in cell origins and evolution.
Abstract.
Author URL.
2022
Cama J, Al Nahas K, Fletcher M, Hammond K, Ryadnov MG, Keyser UF, Pagliara S (2022). An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics.
Scientific Reports,
12(1).
Abstract:
An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics
Antimicrobial resistance challenges the ability of modern medicine to contain infections. Given the dire need for new antimicrobials, polypeptide antibiotics hold particular promise. These agents hit multiple targets in bacteria starting with their most exposed regions—their membranes. However, suitable approaches to quantify the efficacy of polypeptide antibiotics at the membrane and cellular level have been lacking. Here, we employ two complementary microfluidic platforms to probe the structure–activity relationships of two experimental series of polypeptide antibiotics. We reveal strong correlations between each peptide’s physicochemical activity at the membrane level and biological activity at the cellular level. We achieve this knowledge by assaying the membranolytic activities of the compounds on hundreds of individual giant lipid vesicles, and by quantifying phenotypic responses within clonal bacterial populations with single-cell resolution. Our strategy proved capable of detecting differential responses for peptides with single amino acid substitutions between them, and can accelerate the rational design and development of peptide antimicrobials.
Abstract.
Zhang B, Stone MRL, Sanjaya KC, Łapińska U, Pagliara S, Blaskovich MAT (2022). Application of antibiotic-derived fluorescent probes to bacterial studies. In (Ed)
Methods in Enzymology, 1-28.
Abstract:
Application of antibiotic-derived fluorescent probes to bacterial studies
Abstract.
Dimitriu T, Kurilovich E, Łapińska U, Severinov K, Pagliara S, Szczelkun MD, Westra ER (2022). Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition.
Cell Host Microbe,
30(1), 31-40.e5.
Abstract:
Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition.
Phages impose strong selection on bacteria to evolve resistance against viral predation. Bacteria can rapidly evolve phage resistance via receptor mutation or using their CRISPR-Cas adaptive immune systems. Acquisition of CRISPR immunity relies on the insertion of a phage-derived sequence into CRISPR arrays in the bacterial genome. Using Pseudomonas aeruginosa and its phage DMS3vir as a model, we demonstrate that conditions that reduce bacterial growth rates, such as exposure to bacteriostatic antibiotics (which inhibit cell growth without killing), promote the evolution of CRISPR immunity. We demonstrate that this is due to slower phage development under these conditions, which provides more time for cells to acquire phage-derived sequences and mount an immune response. Our data reveal that the speed of phage development is a key determinant of the evolution of CRISPR immunity and suggest that use of bacteriostatic antibiotics can trigger elevated levels of CRISPR immunity in human-associated and natural environments.
Abstract.
Author URL.
Kellom M, Pagliara S, Richards TA, Santoro A (2022). Correction to 'Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments' (2022) by Kellom et al.
Open Biol,
12(9).
Author URL.
Castillo Vila S (2022). Development of Novel Microfluidic Techniques for the Study of Microalgae at the Single-Cell Level.
Abstract:
Development of Novel Microfluidic Techniques for the Study of Microalgae at the Single-Cell Level
Aquatic environments make up 70% of the total Planet Earth surface and marine
phytoplankton is of crucial importance in the regulation of the climate as well as
a key contributor to global geochemical cycles. Although marine microorganisms have
been widely studied during decades, there exists a lack of quantification methods
allowing for their in vivo and single-cell-level investigation. The complexity of the marine
environment considering currents, pycnoclines and other different physicochemical phenomena, makes its recreation a difficult task. In order to overcome such
complexities, we have studied three different microfluidic devices,
here named: (i) Lagoon-like devices, (ii) Classical Mother Machine devices
and (iii) Modified Mother Machine devices. Our main aim was to test the feasibility
of each device in robustly growing Ostreococcus tauri (O. tauri), a model microalga for
studies of alga-virus and alga-bacteria interactions and circadian rhythm.
We successfully followed and observed O. tauri development within the Modified
Mother Machine microfluidic device at the single-cell level. In addition, we also
investigated the different life stages of the microalgal cells with a high image
resolution. We were also able to observe the proliferation of bacteria within all three
devices. This fact, however, the presence of bacteria, became a problem since they
inhibited the normal growth of O. tauri cells.
The main advantage of our system is that it allows for the long-term (up to 10
days) cultivation of single cells of the microalga under a well-controlled
physical environment, as for instance: temperature, light irradiance, and medium supply.
Our system has the potential to provide a single-cell resolution to different fields
within aquatic microbiology, including, cell physiology, climate change effects on
individual cells and the study of microbial interactions.
Abstract.
Kellom M, Pagliara S, Richards TA, Santoro AE (2022). Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments.
Open Biol,
12(7).
Abstract:
Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments.
Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community-Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.
Abstract.
Author URL.
Łapińska U, Voliotis M, Lee KK, Campey A, Stone MRL, Tuck B, Phetsang W, Zhang B, Tsaneva-Atanasova K, Blaskovich MAT, et al (2022). Fast bacterial growth reduces antibiotic accumulation and efficacy.
eLife,
11Abstract:
Fast bacterial growth reduces antibiotic accumulation and efficacy
Phenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here, we hypothesise that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations of Escherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepacia, and Staphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast-growing variants, including efflux that can reduce macrolide accumulation. We used this new knowledge to eradicate variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.
Abstract.
Attrill E (2022). Fighting Infectious Diseases with Antimicrobial Agents using Microfluidic Platforms.
Abstract:
Fighting Infectious Diseases with Antimicrobial Agents using Microfluidic Platforms
The COVID-19 pandemic has demonstrated the impact that untreatable infectious pathogens can have on society but an existing threat, if unaddressed could be even more devastating. Excessive deaths from infectious diseases were thought to be a thing of the past but antimicrobial resistance could cause the 700,000 annual deaths reported from resistant organisms to rise. New or alternative treatments to target Gram-negative pathogens are urgently required, alongside a greater understanding of the mechanisms of resistance to currently available therapeutics. Here I aim to advance the field of antimicrobial research through the exploration of the potential alternative therapy, bacteriophages, as well as investigating novel ways of cultivating previously unidentified antibiotic producing microorganisms.
I demonstrate through novel microfluidic and single cell technologies (previously underutilised for phage assessments) that strategies for phage resistance in Escherichia coli are environment – structure dependent. In more complex environments, bacteria favour phenotypic over genetic resistance, which occurs through a diverse range of mechanisms such as filamentation or reduced receptor expression, and that extensive heterogeneity exists within the population. Such findings are important to enable the evolutionary and ecological dynamics of bacteria–phage interactions to be predicted and manipulated if they are to become a viable therapy in the clinic.
I further show that using these microfluidic systems, the environment where phage-bacteria interactions occur can be tightly moderated and manipulated. Exposure duration, nutrient availability and even bacterial growth phase can be altered to optimise killing efficacy and observe the different single cell phenotypes of both surviving and susceptible cells that occur in response to phage.
New treatments to target potential biothreat agents are also required. Here I have shown novel treatment options for Burkholderia involving a recently environmentally isolated phage in combination with existing antibiotics. Through antibiotic-antibiotic and phage – antibiotic combinations, I have been able to demonstrate improved clearance of B. thailandensis populations in vitro whilst lowering the required concentration of antibiotic.
Although studies involving bacteriophage as an antimicrobial therapy are proving promising, they have not replaced the urgent need for new antibiotics. The majority of our current antibiotics are derived from environmental bacteria, but no new compounds have been licensed for decades. Here culturing platforms were designed to facilitate the growth of previously unculturable bacteria in an estuarine mud environment in situ. This method is still low-through put and additional parallel approaches are required such as microdroplet/ microfluidic systems or culture independent approaches like metagenomics.
Ultimately, the future of antibiotic discovery to target the antibiotic resistance crisis lies in combined, parallel investigations utilising all available knowledge and resources in a unified approach for the treatment of infectious diseases.
Abstract.
Binsley J, Pagliara S, Ogrin F (2022). Numerical Investigation of Flexible Purcell-like Integrated Microfludic Pumps (dataset).
Abstract:
Numerical Investigation of Flexible Purcell-like Integrated Microfludic Pumps (dataset)
The dataset related to the paper titled: Numerical Investigation of Flexible Purcell-like Integrated Microfludic Pumps
Abstract.
Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, et al (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells.
Communications Biology,
5(1).
Abstract:
Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells
AbstractThe interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.
Abstract.
Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, et al (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual bacteria.
2021
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2021). Correction: Microfluidic devices powered by integrated elasto-magnetic pumps.
Lab Chip,
21(15), 3019-3020.
Abstract:
Correction: Microfluidic devices powered by integrated elasto-magnetic pumps.
Correction for 'Microfluidic devices powered by integrated elasto-magnetic pumps' by Jacob L. Binsley et al. Lab Chip, 2020, 20, 4285-4295, DOI:.
Abstract.
Author URL.
Conners R, McLaren M, Łapińska U, Sanders K, Stone MRL, Blaskovich MAT, Pagliara S, Daum B, Rakonjac J, Gold VAM, et al (2021). CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage.
Nature Communications,
12(1).
Abstract:
CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage
AbstractThe Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.
Abstract.
Morrish R, Yim KHW, Pagliara S, Palombo F, Chahwan R, Stone N (2021). Data supporting Morrish et al. (2021) Frontiers in Cell and Developmental Biology.
Palombo F, Pagliara S, Singh A, Chahwan R (2021). Editorial: Probing the Chromatin Architecture.
Front Cell Dev Biol,
9 Author URL.
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2021). Elasto-Magnetic Pumps Integrated within Microfluidic Devices.
Goode O, Smith A, Łapińska U, Bamford R, Kahveci Z, Glover G, Attrill E, Carr A, Metz J, Pagliara S, et al (2021). Heterologous Protein Expression Favors the Formation of Protein Aggregates in Persister and Viable but Nonculturable Bacteria.
ACS Infect Dis,
7(6), 1848-1858.
Abstract:
Heterologous Protein Expression Favors the Formation of Protein Aggregates in Persister and Viable but Nonculturable Bacteria.
Environmental and intracellular stresses can perturb protein homeostasis and trigger the formation and accumulation of protein aggregates. It has been recently suggested that the level of protein aggregates accumulated in bacteria correlates with the frequency of persister and viable but nonculturable cells that transiently survive treatment with multiple antibiotics. However, these findings have often been obtained employing fluorescent reporter strains. This enforced heterologous protein expression facilitates the visualization of protein aggregates but could also trigger the formation and accumulation of protein aggregates. Using microfluidics-based single-cell microscopy and a library of green fluorescent protein reporter strains, we show that heterologous protein expression favors the formation of protein aggregates. We found that persister and viable but nonculturable bacteria surviving treatment with antibiotics are more likely to contain protein aggregates and downregulate the expression of heterologous proteins. Our data also suggest that such aggregates are more basic with respect to the rest of the cell. These findings provide evidence for a strong link between heterologous protein expression, protein aggregation, intracellular pH, and phenotypic survival to antibiotics, suggesting that antibiotic treatments against persister and viable but nonculturable cells could be developed by modulating protein aggregation and pH regulation.
Abstract.
Author URL.
Attrill EL, Claydon R, Łapińska U, Recker M, Meaden S, Brown AT, Westra ER, Harding SV, Pagliara S (2021). Individual bacteria in structured environments rely on phenotypic resistance to phage.
PLoS Biol,
19(10).
Abstract:
Individual bacteria in structured environments rely on phenotypic resistance to phage.
Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria-phage interactions in naturally structured environments.
Abstract.
Author URL.
Łapińska U, Glover G, Kahveci Z, Irwin NAT, Milner DS, Tourte M, Albers S-V, Santoro AE, Richards TA, Pagliara S, et al (2021). Membrane permeability differentiation at the lipid divide.
Martin E (2021). Microfluidic Elasto-Magnetic Materials for Controlled Swimming and Pumping.
Abstract:
Microfluidic Elasto-Magnetic Materials for Controlled Swimming and Pumping
This thesis presents the results from investigating the behavior of different magnetically actuated systems capable of creating motion or activating fluid flow within a low Reynolds number regime. It demonstrates a number of designs where magnetic materials are integrated into elastic networks and the systems are activated by an oscillating magnetic field. The elasto-magnetic systems rely on magnetic and elastic interactions to generate their movement and are designed in such a way as to induce non-reciprocal motion that could be used to manipulate fluid. The thesis demonstrates the capability of these devices and investigates its potential application in microfluidic systems. The presented research is primarily focused on three elasto-magnetic designs.
The first design was based on two interacting ferromagnetic particles with different properties connected by an elastic link. The devices produced were that of a 68 µm microswimmer and a membrane or network spanning 12 mm with feature sizes of the order of micrometers. Ellipsoidal CoNiP (major and minor diameters of 30 µm and 10 µm) and cylindrical Co (diameter 10 µm) particles were produced by electrodeposition. The electrodeposition parameters have been optimised on deposition of CoNiP films to produce an out-plane coercivity for CoNiP elements of 54 kA/m. A fabrication process was created using lithographic techniques to produce a highly structured network of a silicon-based organic polymer, Polydimethylsiloxane (PDMS), embedded with the described magnets. Although this design did not demonstrate active pumping, important conclusions were derived regarding the improvements required to make it more practically suited.
The second design consisted of a series of magnetic discs connected to a frame via elastic axles. The paddles had the same magnetic properties but different elastic properties, due to the different widths of their connecting axles. These introduced a phase difference in the motion of the paddles when actuated. This phase difference was reminiscent of metachronal waves that commonly exist in cilia carpets. In order to understand this design further, a theoretical model was developed and various parameters were investigated, such as frequency and rotational stiffness of the paddles, which was implicative to the width of the axles. For the dimensionless parameters investigated, the maximum speed was generated when the center-to-center separation was 0.9, the frequency was 1.4, lp1= 0.130 and lp2 = 0.225, achieving maximum angles of 45° and 148° respectively.
The third design comprised of only a single ferromagnetic component, which was at the `head' of the device, connected to an asymmetric `tail'. This 3-linked `tail' was inspired by Purcell's 3-link swimmer. The head of the device was actively driven while the elastic links followed. This introduced a phase difference in the generated motion of the device. The 3-linked structure was integrated within a microfluidic device to produce an enclosed pumping system. In this section, the properties of the path drawn by the head during its cycle and the flow rate generated by this device were researched for different fluid viscosities and driving frequencies. It was found that this system could provide a tuneable fluid flow with a flow rate of up to 700 µl/h. The fluid flow was able to be reversed by adjusting the driving frequency.
Abstract.
Morrish R (2021). Monitoring chromatin remodelling in. xed and live immune cells using vibrational spectroscopy and micro uidics.
Abstract:
Monitoring chromatin remodelling in. xed and live immune cells using vibrational spectroscopy and micro uidics
Eukaryotic cell growth, maintenance and differentiation relies on the dynamic structure of nuclear chromatin, the macromolecular complex consisting primarily of DNA and histones. Changes to chromatin structure and chemistry may lead to alterations in gene expression, resulting in functional and developmental processes in cells. Additionally, biomechanical properties of the nucleus, which play a role in mechanical
signalling pathways, are also affected by chromatin conformation. The regulation and effects of chromatin dynamics in cellular processes have yet to be fully elucidated. Therefore, novel techniques for assessing chemical and mechanical signatures of cells undergoing chromatin changes during cell differentiation at the single cell level have great potential for 1) phenotypic characterisation of single cells for research and clinical purposes and 2) further unravelling the complex coordination of intracellular changes that occur during cell developmental steps and triggering of disease.
In this thesis, I have studied chromatin remodelling in immune cells using vibrational spectroscopy and microfluidics. Single cell measurements were conducted through optimisations of experimental and data analysis parameters. Vibrational spectroscopy methods included FTIR spectroscopic imaging and Raman microscopy, both label-free
techniques that measure the interaction of light with chemical properties of a sample by interrogating its molecular vibrations. Microfluidics is a technique for manipulating fluids at a submillimetre scale. It was utilised here to enable live cell Raman mapping, as well as for deformability cytometry for assessing mechanical properties of the cell nuclei. To initiate an immune activation, B cells were incubated with a cytokine (CIT) cocktail.
The biomechanical property, nuclear auxeticity, was investigated in B cells using deformability cytometry. This property has previously been shown in transitioning embryonic stem (ES) cells, and chromatin decondensation has been determined to hold a regulatory role. Chromatin decondensation was therefore induced in B cells through immune activation (CIT treatment) or Trichostatin a (TSA) treatment. These cells were compared to untreated control cells. A subset of cells for both the CIT and TSA treatment, had auxetic nuclei. No control cells had auxetic nuclei. These results showed nuclear auxeticity in B cells for the fi rst time, and linked it to chromatin decondensation in agreement with previous ES cell data.
Using FTIR spectroscopic imaging and Raman microscopy, spectral features associated with chromatin and DNA changes during immune B cell activation were identifi ed. Peak ratios for distinguishing between non-activated and activated immune cells were determined - for FTIR imaging: a DNA-to-protein peak ratio, and for Raman mapping: a peak ratio between two neighbouring peaks, both associated with nucleic acid. Both peak ratios measured the relative change in a peak associated with
νs(PO2-), which was therefore shown to be a potential spectral marker for label-free characterisation of immune cells pre- and post activation. The biological origin of the FTIR spectral features was further investigated using additional cell treatments. Chromatin decondensation, intiated through CIT or TSA treatment, gave rise to similar change in the DNA-to-protein peak ratio. This supported the hypothesis that the νs(PO2-) spectral changes can be used to monitor structural changes occurring in chromatin and DNA itself.
Finally, the key biological pathways in influencing the whole range of Raman spectral differences between non-activated and activated B cells were investigated. Partial least squares (PLS) regression was performed on Raman maps and transcriptomic data. It was determined that a linear correlation exists between the two data types. Transcripts of high importance for this correlation were identifi ed. These included the
B cell receptor genes and a number of transcripts of regulatory proteins with known roles in immune activation. Transcripts not previously linked to immune activation were also identi fied.
In summary, novel techniques for phenotypic characterisation of single cells were explored using both chemical and mechanical measurements of B cells undergoing immune activation. Previously unidenti fied biochemical and biomechanical factors influencing B cell activation were identifi ed. These have added new layers to our understanding
of this process and thus revealed potential new research directions. Furthermore, chromatin decondensation and transcriptional changes are key responses during all cell differentiation processes and disease development. Therefore, these experimental approaches have great potential for investigating other cell types and cellular processes.
Abstract.
Goode O, Smith A, Zarkan A, Cama J, Invergo BM, Belgami D, Caño-Muñiz S, Metz J, O’Neill P, Jeffries A, et al (2021). Persister Escherichia coli Cells Have a Lower Intracellular pH than Susceptible Cells but Maintain Their pH in Response to Antibiotic Treatment.
mBio,
12(4).
Abstract:
Persister Escherichia coli Cells Have a Lower Intracellular pH than Susceptible Cells but Maintain Their pH in Response to Antibiotic Treatment
Persister and VBNC cells can phenotypically survive environmental stressors, such as antibiotic treatment, limitation of nutrients, and acid stress, and have been linked to chronic infections and antimicrobial resistance. It has recently been suggested that pH regulation might play a role in an organism’s phenotypic survival to antibiotics; however, this hypothesis remains to be tested.
Abstract.
Morrish R, Yim KHW, Pagliara S, Palombo F, Chahwan R, Stone N (2021). Single cell label-free probing of chromatin dynamics during B lymphocyte maturation.
Hammond K, Cipcigan F, Al Nahas K, Losasso V, Lewis H, Cama J, Martelli F, Simcock PW, Fletcher M, Ravi J, et al (2021). Switching Cytolytic Nanopores into Antimicrobial Fractal Ruptures by a Single Side Chain Mutation. ACS Nano
2020
Gironi B, Kahveci Z, McGill B, Lechner B-D, Pagliara S, Metz J, Morresi A, Palombo F, Sassi P, Petrov PG, et al (2020). Effect of DMSO on the Mechanical and Structural Properties of Model and Biological Membranes. Biophysical Journal, 119(2), 274-286.
Kepiro IE, Marzuoli I, Hammond K, Ba X, Lewis H, Shaw M, Gunnoo SB, De Santis E, Łapińska U, Pagliara S, et al (2020). Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters.
ACS Nano,
14(2), 1609-1622.
Abstract:
Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters.
Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.
Abstract.
Author URL.
Stone MRL, Łapińska U, Pagliara S, Masi M, Blanchfield JT, Cooper MA, Blaskovich MAT (2020). Fluorescent macrolide probes – synthesis and use in evaluation of bacterial resistance.
RSC Chemical Biology,
1(5), 395-404.
Abstract:
Fluorescent macrolide probes – synthesis and use in evaluation of bacterial resistance
Macrolide fluorescent probes illuminate the interactions between antibiotics and bacteria, providing new insight into mechanisms of resistance.
Abstract.
Ahmed J (2020). Investigating the Effect of Temperature on Pump-Driven Antibiotic Resistance towards Erythromycin in Escherichia coli.
Abstract:
Investigating the Effect of Temperature on Pump-Driven Antibiotic Resistance towards Erythromycin in Escherichia coli
Antibiotic resistance is an inevitable by-product from treatment of bacterial (and fungal) infections, however the rate and intensity at which it is emerging is alarming. More and more drugs are being rendered ineffective, where poor treatment behaviours, such as overuse, are being held accountable. Coupled with a dry antibiotic pipeline, we are increasingly seeing ourselves approach a post-antibiotic era. As research is being conducted into discovering new antibiotics, we also need to find ways to preserve the ones we still have. Therefore it is equally important to identify and study potential selection pressures, both environmental and clinical, that contribute to the rise in resistance.
To provide a preliminary insight on temperature as a possible selection pressure, this research project aimed to investigate the effect of temperature on the susceptibility of Escherichia coli to the macrolide-class antibiotic erythromycin, and ultimately its effect on the expression of multidrug efflux pump AcrAB-TolC. This was done by exposing E. coli cells to a range of erythromycin concentrations during 24 hours of growth, establishing a minimum inhibitory concentration (MIC) at 30°C and seeing any shifts in the MIC at 37°C. It was found that as temperature increased from 30°C to 37°C, so did the MIC. Thus the cells were more resistant at the higher temperature.
Next, to see whether and how AcrAB-TolC was selected for as a result of temperature, the expression of protein AcrB was measured via fluorescence emitted from sfGFP (due to the sfGFP gene being physically fused to the acrB gene). It was found that the range of concentrations that select for pump expression, referred to as the “AcrB expression-selection window”, shifted positively with increasing temperature. This suggests a temperature-dependent nature of resistance selection, therefore this knowledge may help in choosing an effective dose for treatment based on thermal conditions.
The outcomes of this research project will help provide a foundation for looking further into temperature, and other selection pressures, and their effect on the rise in antibiotic resistance.
Abstract.
Kaczmar A (2020). Investigating the dynamics of expression of persister genes in Escherichia coli responding to environmental changes.
Abstract:
Investigating the dynamics of expression of persister genes in Escherichia coli responding to environmental changes
Antibiotics have been a one of the many wonders of modern medicine, improving life quality and saving lives on daily basis. Their misuse has caused decreased efficacy worldwide, which is becoming a serious public health threat. An important aspect of decreased antimicrobial efficacy is antibiotic tolerance, of which persisters and Viable but not Culturable (VBNC) cells are important examples: they survive the antibiotic treatment and can give rise to a new population. Therefore, their presence in otherwise susceptible cultures has been implied in recurring infections, threatening safety of food and of water supplies. So far, no obvious markers for these cells have been identified. These tolerant cells appear randomly in bacterial populations, but their existence is also a form of adaptation to environmental challenges, like the presence of antimicrobial drugs. Independently from their susceptibility, all bacterial cells must constantly fine tune their responses to such challenges, and to interact with their surroundings. Signals from the external environment are transmitted across signalling pathways and influence bacterial gene expression. RNA in its different forms, like mRNA, is the link of this communication between the external world and the cell’s DNA. For this project, RNA was extracted during the lag phase of Escherichia coli BW25113 (wild type) growth in LB medium. Examples of transcriptomics results presented here show that E. coli respond to changes in the culture conditions, like medium temperature and pH. This work also presents a protocol for RNA extractions from E. coli persisters and VBNC cells in exponential phase, after 3 hours of challenge with ampicillin. They did not yield consistent results in terms of RNA quantity but could become a steppingstone to further investigation of the tolerant phenotypes in E. coli.
Abstract.
Cama J, Pagliara S (2020). Microfluidic Single-Cell Phenotyping of the Activity of Peptide-Based Antimicrobials. In Ryadnov M (Ed) Polypeptide Materials, Humana, New York, NY, 237-253.
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2020). Microfluidic devices powered by elasto-magnetic pumps (dataset).
Abstract:
Microfluidic devices powered by elasto-magnetic pumps (dataset)
This is the dataset used for the Binsley et al. (2020) article "Microfluidic devices powered by elasto-magnetic pumps" published in Lab on a Chip.
Abstract.
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2020). Microfluidic devices powered by integrated elasto-magnetic pumps.
Lab on a Chip,
20(22), 4285-4295.
Abstract:
Microfluidic devices powered by integrated elasto-magnetic pumps
Integrated elasto-magnetic pumps power portable microfluidic devices for point of care testing.
Abstract.
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2020). Microfluidic devices powered by integrated elasto-magnetic pumps (dataset).
Abstract:
Microfluidic devices powered by integrated elasto-magnetic pumps (dataset)
This is the dataset used for the Binsley et al. (2020) article "Microfluidic devices powered by integrated elasto-magnetic pumps" published in Lab on a Chip.
Abstract.
Binsley JL, Martin EL, Myers TO, Pagliara S, Ogrin FY (2020). Microfluidic devices powered by integrated elasto-magnetic pumps (dataset).
Cama J, Voliotis M, Metz J, Smith A, Iannucci J, Keyser UF, Tsaneva K, Pagliara S (2020). Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. Lab on a Chip
Valente F (2020). Sub-cellular responses of wheat epidermal cells to Zymoseptoria tritici.
Abstract:
Sub-cellular responses of wheat epidermal cells to Zymoseptoria tritici
Zymoseptoria tritici (formerly Mycosphaerella graminicola), an Ascomycete fungus, is the main causal agent of Septoria tritici blotch, one of the main devastating wheat (Triticum aestivum) foliar diseases worldwide. The infection cycle of the hemi-biotrophic Z. tritici is divided into a symptom-less biotrophic phase followed by a necrotrophic phase characterised by pycnidia development. Little is known about molecular and cellular strategies of wheat defence during the first intimate contact with Z. tritici. Furthermore, information about immune responses in the wheat epidermal cells in pre-invasion resistance is lacking. In order to address the questions outlined above, we designed a series of novel assays on this plant patho-system to analyse the role of wheat focal immunity in response to Z. tritici hyphae. We tested the hypothesis that these wheat sub-cellular responses differed between Z. tritici virulent and avirulent strains during the fungal biotrophic symptom-less phase. High-resolution microscopy approaches combined with automated object detection recognition for organelle movement suggested a response from subsidiary cells flanking guard cells in the Z. tritici pre-invasion defence with regards to early changes of cell wall architecture and organelle re-distribution at the site of fungal interaction. These responses showed only subtle differences between compatible and incompatible strain-cultivar combinations. Our preliminary evidence suggests that the presence or absence of focal responses in subsidiary cells does not depend upon the AvrStb6 / Stb6 gene-for-gene relationship. Thus, novel applications in biology combined with live-cell imaging provided us with a promising tool to analyse the spatiotemporal dynamics of Z. tritici hyphae on infected wheat tissues. To the extent of our knowledge, this is the first report that analyses wheat subsidiary cells in response to fungal pathogens at the sub-cellular scale. This may constitute the object of future studies of wheat immunity and drive to the discovery of key factors linked to the strategies that lead to fungal invasion and circumvention of the wheat immune system.
Abstract.
Stie MB, Corezzi M, Juncos Bombin AD, Ajalloueian F, Attrill E, Pagliara S, Jacobsen J, Chronakis IS, Nielsen HM, Foderà V, et al (2020). Waterborne Electrospinning of α-Lactalbumin Generates Tunable and Biocompatible Nanofibers for Drug Delivery.
ACS Applied Nano Materials,
3(2), 1910-1921.
Abstract:
Waterborne Electrospinning of α-Lactalbumin Generates Tunable and Biocompatible Nanofibers for Drug Delivery
Protein-based drug carriers are an interesting alternative to traditional polymeric drug delivery systems due to their intrinsic biocompatibility and biodegradability. Electrospinning of neat proteins holds advantages over electrospinning of protein mixtures, e.g. whey isolates, such as better control of the physicochemical and biological function of the resulting nanofiber-based system. In this study, we explore electrospinning of the isolated milk protein α-lactalbumin (ALA), which is a whey protein with important nutritional and pharmacological properties. Via waterborne electrospinning of ALA with a minimum amount of poly(ethylene oxide) (PEO) as a cospininng polymer, nanofibers of high protein content were successfully produced (up to 84% (w/w)). We demonstrate the ability to produce ALA-based nanofibers with a high degree of tunability in terms of size, stability in water, and mechanical properties. The nanofibers displayed excellent biocompatibility in vitro as the viability of cultured TR146 human buccal epithelium and NIH 3T3 murine fibroblast cells was not influenced by exposure to ALA-based nanofibers. ALA-based nanofibers were loaded with up to 6% (w/w) ampicilin, and the nanofibers were capable of maintaining the activity of the antibiotic after electrospinning and cross-linking. Using such a property of the material, we demonstrate that ampicillin-loaded nanofibers successfully inhibit the growth of Gram-negative bacteria in vitro. Importantly, after treatment with ampicillin-loaded nanofibers, no bacterial regrowth was observed, which indicates that this treatment may clear eventual persisters to ampicillin. Finally, the structural properties of the native functional protein were maintained after release of ALA from the nanofibers. This promotes our platform, not only as a sustainable protein-based drug delivery system, but also as an innovative solid form of ALA for food and pharmaceutical applications.
Abstract.
2019
Martin EL, Bryan MT, Pagliara S, Ogrin FY (2019). Advanced Processing of Micropatterned Elasto-Magnetic Membranes. IEEE Transactions on Magnetics
Blaskovich MA, Phetsang W, Stone MRL, Lapinska U, Pagliara S, Bhalla R, Cooper MA (2019). Antibiotic-derived molecular probes for bacterial imaging.
Abstract:
Antibiotic-derived molecular probes for bacterial imaging
Abstract.
Łapińska U, Glover G, Capilla-Lasheras P, Young AJ, Pagliara S (2019). Bacterial ageing in the absence of external stressors.
Philosophical Transactions of the Royal Society B: Biological Sciences,
374(1786), 20180442-20180442.
Abstract:
Bacterial ageing in the absence of external stressors
. Evidence of ageing in the bacterium
. Escherichia coli
. was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in
. E. coli
. in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the ‘maternal old pole’ progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context.
.
. This article is part of a discussion meeting issue ‘Single cell ecology’.
Abstract.
Smith A, Metz J, Pagliara S (2019). MMHelper: an automated framework for the analysis of microscopy images acquired with the mother machine.
Sci Rep,
9(1).
Abstract:
MMHelper: an automated framework for the analysis of microscopy images acquired with the mother machine.
Live-cell imaging in microfluidic devices now allows the investigation of cellular heterogeneity within microbial populations. In particular, the mother machine technology developed by Wang et al. has been widely employed to investigate single-cell physiological parameters including gene expression, growth rate, mutagenesis, and response to antibiotics. One of the advantages of the mother machine technology is the ability to generate vast amounts of images; however, the time consuming analysis of these images constitutes a severe bottleneck. Here we overcome this limitation by introducing MMHelper ( https://doi.org/10.5281/zenodo.3254394 ), a publicly available custom software implemented in Python which allows the automated analysis of brightfield or phase contrast, and any associated fluorescence, images of bacteria confined in the mother machine. We show that cell data extracted via MMHelper from tens of thousands of individual cells imaged in brightfield are consistent with results obtained via semi-automated image analysis based on ImageJ. Furthermore, we benchmark our software capability in processing phase contrast images from other laboratories against other publicly available software. We demonstrate that MMHelper has over 90% detection efficiency for brightfield and phase contrast images and provides a new open-source platform for the extraction of single-bacterium data, including cell length, area, and fluorescence intensity.
Abstract.
Author URL.
Lutz T (2019). New optical super-resolution imaging approaches involving DNA nanotechnology.
Abstract:
New optical super-resolution imaging approaches involving DNA nanotechnology
With recent advances in optical super-resolution microscopy, biological structures can be imaged with single-nanometre resolution using visible light. One implementation thereof, DNA-PAINT (Point Accumulation for Imaging in Nano-scale Topography), is based on the highly specific and transient binding of fluorescently labelled oligonucleotides, the "imager strands", to complementary strands with which the targets are labelled, the "docking strands". The imager-docking binding events are detected as fluorescence blinking and can be localised with single-nanometre precision. From the set of localised events a super-resolution image can be assembled. DNA-PAINT has multiple advantages over other imaging methods, e.g. high photon yields resulting in high resolution, a free choice of fluorophores while being effectively free from photobleaching, straightforward implementation on a conventional fluorescence microscope and the possibility of temporally multiplexed and quantitative imaging.
In this thesis, a test sample based on functionalised microspheres is developed, which allows for optimisation of various DNA-PAINT imaging parameters and for the characterisation and testing of new variations and modifications of DNA-PAINT. One such method which was developed for this thesis, Quencher-Exchange-PAINT, facilitates temporally multiplexed imaging, which is based on the sequential exchange of imager strands targeting different docking strands. The exchange step is replaced by addition of competitive quencher-strands, allowing for rapid, low-crosstalk imager exchange even in biological samples with limited diffusion. Additionally, Proximity-Dependent PAINT is introduced, which enables the imaging of the nanoscale distribution of protein pairs by interaction of two proximity probes which activates DNA-PAINT type binding. The technique is demonstrated both on the microsphere assay as well as in biological samples. Finally, approaches for enhancing the signal-to-noise ratio are explored.
Abstract.
Smith A (2019). Novel technologies to study single-cell response to environmental stimuli.
Abstract:
Novel technologies to study single-cell response to environmental stimuli
Antibiotic tolerant phenotypes, such as persister and viable but non culturable cells (VBNC), are known to be present in isogenic bacterial populations. These phenotypes are now recognised as an important factor in the recalcitrance of infections and the development of antibiotic resistance; which itself is currently a major global health crisis. However, despite their clinical importance, we still know little about the mechanisms behind their formation and the relationship between the two phenotypes. Due to the relatively low abundance of the two phenotypes within the population and, in the case of VBNC cells, their ability to remain dormant for extended periods of time, high throughput single cell approaches currently provide the best opportunities for investigating them; in particular microfluidics has emerged as an exciting platform for investigating phenotypic heterogeneity at the single cell level due to the control it allows of the extracellular environment.
Using antibiotic persistence as a proxy, we identify temporal windows in which a growing E. coli population exhibits significant changes in phenotypic heterogeneity and determine highly regulated genes and pathways at the population level. We then develop a high throughput microfluidic protocol, based on the pre-existing Mother Machine device, to investigate persister and VBNC cells before, during and after antibiotic exposure at the single cell level. We then developed the first fully automated image analysis pipeline that is capable of analysing Mother Machine images acquired in both bright field and phase contrast imaging modalities. The combination of our protocol and image analysis software allowed us to investigate the role of the previously identified genes in the formation of antibiotic persister and VBNC cells, where we identify potential biomarkers for these phenotypes before exposure to antibiotic. We then used the microfluidic set up to investigate the relationship between protein aggregation and antibiotic persister and VBNC cells. We find that protein aggregation can be correlated to the expression of exogenous proteins and that cells containing visible protein aggregates are, in turn, more likely to be persister or VBNC cells; providing further evidence that these phenotypes are not distinct and are instead part of one physiological continuum.
Abstract.
Richards TA, Massana R, Pagliara S, Hall N (2019). Single cell ecology.
Philos Trans R Soc Lond B Biol Sci,
374(1786).
Abstract:
Single cell ecology.
Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue 'Single cell ecology'.
Abstract.
Author URL.
Brandstrup Morrish R, Hermes M, Metz J, Stone N, Pagliara S, Chahwan R, Palombo F (2019). Single cell imaging of nuclear architecture changes. Frontiers in Immunology, 7, 1-14.
2018
Smith A, Kaczmar A, Bamford RA, Smith C, Frustaci S, Kovacs-Simon A, O'Neill P, Moore K, Paszkiewicz K, Titball RW, et al (2018). The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli.
FRONTIERS IN MICROBIOLOGY,
9 Author URL.
Lutz T, Clowsley AH, Lin R, Pagliara S, Di Michele L, Soeller C (2018). Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT.
Nano Research,
11(12), 6141-6154.
Abstract:
Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT
The optical super-resolution technique DNA-PAINT (Point Accumulation Imaging in Nanoscale Topography) provides a flexible way to achieve imaging of nanoscale structures at ∼10-nanometer resolution. In DNA-PAINT, fluorescently labeled DNA “imager” strands bind transiently and with high specificity to complementary target “docking” strands anchored to the structure of interest. The localization of single binding events enables the assembly of a super-resolution image, and this approach effectively circumvents photobleaching. The solution exchange of imager strands is the basis of Exchange-PAINT, which enables multiplexed imaging that avoids chromatic aberrations. Fluid exchange during imaging typically requires specialized chambers or washes, which can disturb the sample. Additionally, diffusional washout of imager strands is slow in thick samples such as biological tissue slices. Here, we introduce Quencher-Exchange-PAINT—a new approach to Exchange-PAINT in regular open-top imaging chambers—which overcomes the comparatively slow imager strand switching via diffusional imager washout. Quencher-Exchange-PAINT uses “quencher” strands, i.e. oligonucleotides that prevent the imager from binding to the targets, to rapidly reduce unwanted single-stranded imager concentrations to negligible levels, decoupled from the absolute imager concentration. The quencher strands contain an effective dye quencher that reduces the fluorescence of quenched imager strands to negligible levels. We characterized Quencher-Exchange-PAINT when applied to synthetic, cellular, and thick tissue samples. Quencher-Exchange-PAINT opens the way for efficient multiplexed imaging of complex nanostructures, e.g. in thick tissues, without the need for washing steps. [Figure not available: see fulltext.].
Abstract.
2017
Hodgson AC, Verstreken CM, Fisher CL, Keyser UF, Pagliara S, Chalut KJ (2017). A microfluidic device for characterizing nuclear deformations.
Lab Chip,
17(5), 805-813.
Abstract:
A microfluidic device for characterizing nuclear deformations.
Cell nuclei experience and respond to a wide range of forces, both in vivo and in vitro. In order to characterize the nuclear response to physical stress, we developed a microfluidic chip and used it to apply mechanical stress to live cells and measure their nuclear deformability. The device design is optimized for the detection of both nucleus and cytoplasm, which can then be conveniently quantified using a custom-written Matlab program. We measured nuclear sizes and strains of embryonic stem cells, for which we observed negative Poisson ratios in the nuclei. In addition, we were able to detect changes in the nuclear response after treatment with actin depolymerizing and chromatin decondensing agents. Finally, we showed that the device can be used for biologically relevant high-resolution confocal imaging of cells under compression. Thus, the device presented here allows for accurate physical phenotyping at high throughput and has the potential to be applied to a range of cell types.
Abstract.
Author URL.
Bamford RA, Smith A, Metz J, Glover G, Titball RW, Pagliara S (2017). Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy.
BMC Biology,
15(1).
Abstract:
Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy
Background: Clonal microbial populations often harbor rare phenotypic variants that are typically hidden within the majority of the remaining cells, but are crucial for the population's resilience to external perturbations. Persister and viable but non-culturable (VBNC) cells are two important clonal bacterial subpopulations that can survive antibiotic treatment. Both persister and VBNC cells pose a serious threat to human health. However, unlike persister cells, which quickly resume growth following drug removal, VBNC cells can remain non-growing for prolonged periods of time, thus eluding detection via traditional microbiological assays. Therefore, understanding the molecular mechanisms underlying the formation of VBNC cells requires the characterization of the clonal population with single-cell resolution. A combination of microfluidics, time-lapse microscopy, and fluorescent reporter strains offers the perfect platform for investigating individual cells while manipulating their environment. Methods: Here, we report a novel single-cell approach to investigate VBNC cells. We perform drug treatment, bacterial culturing, and live/dead staining in series by using transcriptional reporter strains and novel adaptations to the mother machine technology. Since we track each cell throughout the experiment, we are able to quantify the size, morphology and fluorescence that each VBNC cell displayed before, during and after drug treatment. Results: We show that VBNC cells are not dead or dying cells but share similar phenotypic features with persister cells, suggesting a link between these two subpopulations, at least in the Escherichia coli strain under investigation. We strengthen this link by demonstrating that, before drug treatment, both persister and VBNC cells can be distinguished from the remainder of the population by their lower fluorescence when using a reporter strain for tnaC, encoding the leader peptide of the tnaCAB operon responsible for tryptophan metabolism. Conclusion: Our data demonstrates the suitability of our approach for studying the physiology of non-growing cells in response to external perturbations. Our approach will allow the identification of novel biomarkers for the isolation of VBNC and persister cells and will open new opportunities to map the detailed biochemical makeup of these clonal subpopulations.
Abstract.
Tan Y, Dagdug L, Gladrow J, Keyser UF, Pagliara S (2017). Particle transport across a channel via an oscillating potential.
Phys. Rev. E,
96Abstract:
Particle transport across a channel via an oscillating potential
Membrane protein transporters alternate their substrate-binding sites between
the extracellular and cytosolic side of the membrane according to the
alternating access mechanism. Inspired by this intriguing mechanism devised by
nature, we study particle transport through a channel coupled with an energy
well that oscillates its position between the two entrances of the channel. We
optimize particle transport across the channel by adjusting the oscillation
frequency. At the optimal oscillation frequency, the translocation rate through
the channel is a hundred times higher with respect to free diffusion across the
channel. Our findings reveal the effect of time dependent potentials on
particle transport across a channel and will be relevant for membrane transport
and microfluidics application.
Abstract.
Author URL.
Tan Y, Dagdug L, Gladrow J, Keyser UF, Pagliara S (2017). Particle transport across a channel via an oscillating potential.
2016
Cama J, Schaich M, Al Nahas K, Hernández-Ainsa S, Pagliara S, Keyser UF (2016). Direct Optofluidic Measurement of the Lipid Permeability of Fluoroquinolones.
Sci Rep,
6Abstract:
Direct Optofluidic Measurement of the Lipid Permeability of Fluoroquinolones.
Quantifying drug permeability across lipid membranes is crucial for drug development. In addition, reduced membrane permeability is a leading cause of antibiotic resistance in bacteria, and hence there is a need for new technologies that can quantify antibiotic transport across biological membranes. We recently developed an optofluidic assay that directly determines the permeability coefficient of autofluorescent drug molecules across lipid membranes. Using ultraviolet fluorescence microscopy, we directly track drug accumulation in giant lipid vesicles as they traverse a microfluidic device while exposed to the drug. Importantly, our measurement does not require the knowledge of the octanol partition coefficient of the drug - we directly determine the permeability coefficient for the specific drug-lipid system. In this work, we report measurements on a range of fluoroquinolone antibiotics and find that their pH dependent lipid permeability can span over two orders of magnitude. We describe various technical improvements for our assay, and provide a new graphical user interface for data analysis to make the technology easier to use for the wider community.
Abstract.
Author URL.
Locatelli E, Pierno M, Baldovin F, Orlandini E, Tan Y, Pagliara S (2016). Single-File Escape of Colloidal Particles from Microfluidic Channels.
Physical Review Letters,
117(3).
Abstract:
Single-File Escape of Colloidal Particles from Microfluidic Channels
Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount to quantify the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy, and theoretical analysis we uncover the self-similar character of the escape process and provide closed-formula evaluations of the escape time. We find that the escape time scales inversely with the diffusion coefficient of the last particle to leave the channel. Importantly, we find that at the investigated microscale, bias forces as tiny as 10-15 N determine the magnitude of the escape time by drastically reducing interparticle collisions. Our findings provide crucial guidelines to optimize the design of micro- and nanodevices for a variety of applications including drug delivery, particle filtering, and transport in geometrical constrictions.
Abstract.
Locatelli E, Pierno M, Baldovin F, Orlandini E, Tan Y, Pagliara S (2016). Single-file escape of colloidal particles from microfluidic channels.
2015
Misiunas K, Pagliara S, Lauga E, Lister JR, Keyser UF (2015). Non-decaying hydrodynamic interactions along narrow channels.
Misiunas K, Pagliara S, Lauga E, Lister JR, Keyser UF (2015). Non-decaying hydrodynamic interactions along narrow channels.
Phys. Rev. Lett.,
115Abstract:
Non-decaying hydrodynamic interactions along narrow channels
Particle-particle interactions are of paramount importance in every
multi-body system as they determine the collective behaviour and coupling
strength. Many well-known interactions like electro-static, van der Waals or
screened Coulomb, decay exponentially or with negative powers of the particle
spacing r. Similarly, hydrodynamic interactions between particles undergoing
Brownian motion decay as 1/r in bulk, and are assumed to decay in small
channels. Such interactions are ubiquitous in biological and technological
systems. Here we confine two particles undergoing Brownian motion in narrow,
microfluidic channels and study their coupling through hydrodynamic
interactions. Our experiments show that the hydrodynamic particle-particle
interactions are distance-independent in these channels. This finding is of
fundamental importance for the interpretation of experiments where dense
mixtures of particles or molecules diffuse through finite length, water-filled
channels or pore networks.
Abstract.
Author URL.
Cama J, Bajaj H, Pagliara S, Maier T, Braun Y, Winterhalter M, Keyser UF (2015). Quantification of Fluoroquinolone Uptake through the Outer Membrane Channel OmpF of Escherichia coli.
J Am Chem Soc,
137(43), 13836-13843.
Abstract:
Quantification of Fluoroquinolone Uptake through the Outer Membrane Channel OmpF of Escherichia coli.
Decreased drug accumulation is a common cause of antibiotic resistance in microorganisms. However, there are few reliable general techniques capable of quantifying drug uptake through bacterial membranes. We present a semiquantitative optofluidic assay for studying the uptake of autofluorescent drug molecules in single liposomes. We studied the effect of the Escherichia coli outer membrane channel OmpF on the accumulation of the fluoroquinolone antibiotic, norfloxacin, in proteoliposomes. Measurements were performed at pH 5 and pH 7, corresponding to two different charge states of norfloxacin that bacteria are likely to encounter in the human gastrointestinal tract. At both pH values, the porins significantly enhance drug permeation across the proteoliposome membranes. At pH 5, where norfloxacin permeability across pure phospholipid membranes is low, the porins increase drug permeability by 50-fold on average. We estimate a flux of about 10 norfloxacin molecules per second per OmpF trimer in the presence of a 1 mM concentration gradient of norfloxacin. We also performed single channel electrophysiology measurements and found that the application of transmembrane voltages causes an electric field driven uptake in addition to concentration driven diffusion. We use our results to propose a physical mechanism for the pH mediated change in bacterial susceptibility to fluoroquinolone antibiotics.
Abstract.
Author URL.
Otto O, Rosendahl P, Mietke A, Golfier S, Herold C, Klaue D, Girardo S, Pagliara S, Ekpenyong A, Jacobi A, et al (2015). Real-time deformability cytometry: On-the-fly cell mechanical phenotyping.
Nature Methods,
12(3), 199-202.
Abstract:
Real-time deformability cytometry: On-the-fly cell mechanical phenotyping
We introduce real-time deformability cytometry (RT-DC) for continuous cell mechanical characterization of large populations (>100,000 cells) with analysis rates greater than 100 cells/s. RT-DC is sensitive to cytoskeletal alterations and can distinguish cell-cycle phases, track stem cell differentiation into distinct lineages and identify cell populations in whole blood by their mechanical fingerprints. This technique adds a new marker-free dimension to flow cytometry with diverse applications in biology, biotechnology and medicine.
Abstract.
2014
Cama J, Chimerel C, Pagliara S, Javer A, Keyser UF (2014). A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes.
Lab Chip,
14(13), 2303-2308.
Abstract:
A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes.
With the rise in antibiotic resistance amongst pathogenic bacteria, the study of antibiotic activity and transport across cell membranes is gaining widespread importance. We present a novel, label-free microfluidic assay that quantifies the permeability coefficient of a broad spectrum fluoroquinolone antibiotic, norfloxacin, across lipid membranes using the UV autofluorescence of the drug. We use giant lipid vesicles as highly controlled model systems to study the diffusion through lipid membranes. Our technique directly determines the permeability coefficient without requiring the measurement of the partition coefficient of the antibiotic.
Abstract.
Author URL.
Dettmer SL, Pagliara S, Misiunas K, Keyser UF (2014). Anisotropic diffusion of spherical particles in closely confining. microchannels.
Physical Review E,
98Abstract:
Anisotropic diffusion of spherical particles in closely confining. microchannels
We present here the measurement of the diffusivity of spherical particles
closely confined by narrow microchannels. Our experiments yield a
two-dimensional map of the position-dependent diffusion coefficients parallel
and perpendicular to the channel axis with a resolution down to 129 nm. The
diffusivity was measured simultaneously in the channel interior, the bulk
reservoirs, as well as the channel entrance region. In the channel interior we
found strongly anisotropic diffusion. While the perpendicular diffusion
coefficient close to the confining walls decreased down to approximately 25% of
the value on the channel axis, the parallel diffusion coefficient remained
constant throughout the entire channel width. In addition to the experiment, we
performed finite element simulations for the diffusivity in the channel
interior and found good agreement with the measurements. Our results reveal the
distinctive influence of strong confinement on Brownian motion, which is of
significance to microfluidics as well as quantitative models of facilitated
membrane transport.
Abstract.
Author URL.
Dettmer SL, Pagliara S, Misiunas K, Keyser UF (2014). Anisotropic diffusion of spherical particles in closely confining. microchannels.
Pagliara S, Franze K, McClain CR, Wylde GW, Fisher CL, Franklin RJM, Kabla AJ, Keyser UF, Chalut KJ (2014). Auxetic nuclei in embryonic stem cells exiting pluripotency.
Nature Materials,
13(6), 638-644.
Abstract:
Auxetic nuclei in embryonic stem cells exiting pluripotency
Embryonic stem cells (ESCs) self-renew in a state of naïve pluripotency in which they are competent to generate all somatic cells. It has been hypothesized that, before irreversibly committing, ESCs pass through at least one metastable transition state. This transition would represent a gateway for differentiation and reprogramming of somatic cells. Here, we show that during the transition, the nuclei of ESCs are auxetic: they exhibit a cross-sectional expansion when stretched and a cross-sectional contraction when compressed, and their stiffness increases under compression. We also show that the auxetic phenotype of transition ESC nuclei is driven at least in part by global chromatin decondensation. Through the regulation of molecular turnover in the differentiating nucleus by external forces, auxeticity could be a key element in mechanotransduction. Our findings highlight the importance of nuclear structure in the regulation of differentiation and reprogramming. © 2014 Macmillan Publishers Limited.
Abstract.
Pagliara S, Dettmer SL, Keyser UF (2014). Channel-facilitated diffusion boosted by particle binding at the channel entrance.
Physical Review Letters,
113(4).
Abstract:
Channel-facilitated diffusion boosted by particle binding at the channel entrance
We investigate single-file diffusion of Brownian particles in arrays of closely confining microchannels permeated by a variety of attractive optical potentials and connecting two baths with equal particle concentration. We simultaneously test free diffusion in the channel, diffusion in optical traps coupled in the center of the channel, and diffusion in traps extending into the baths. We found that both classes of attractive optical potentials enhance the translocation rate through the channel with respect to free diffusion. Surprisingly, for the latter class of potentials we measure a 40-fold enhancement in the translocation rate with respect to free diffusion and find a sublinear power law dependence of the translocation rate on the average number of particles in the channel. Our results reveal the function of particle binding at the channel entrances for diffusive transport and open the way to a better understanding of membrane transport and design of synthetic membranes with enhanced diffusion rate. © 2014 American Physical Society.
Abstract.
Pagliara S, Dettmer SL, Misiunas K, Lea L, Tan Y, Keyser UF (2014). Diffusion coefficients and particle transport in synthetic membrane channels.
European Physical Journal: Special Topics,
223(14), 3145-3163.
Abstract:
Diffusion coefficients and particle transport in synthetic membrane channels
Diffusion in constrained geometries is paramount to transport across biological membranes and in mesoporous materials. Although the transported species vary from system to system, the underlying physical mechanisms are universal. However, there is an imbalance between theory and quantitative experimental model systems. We have recently introduced a new synthetic approach to mimic molecular diffusion based on colloidal particles, digital video microscopy, particle tracking, microfluidics and holographic optical tweezers. In this paper we report useful guidelines for the fabrication, handling and characterisation of the microfluidic chips and a study of diffusion coefficients, particle attempt and translocation rates through microfluidic channels with cross sections of different dimensions.
Abstract.
Dettmer SL, Keyser UF, Pagliara S (2014). Local characterization of hindered Brownian motion by using digital. video microscopy and 3D particle tracking.
Dettmer SL, Keyser UF, Pagliara S (2014). Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking.
Rev Sci Instrum,
85(2).
Abstract:
Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking.
In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g. electrokinetic or dielectrophoretic forces.
Abstract.
Author URL.
Schleicher KD, Dettmer SL, Kapinos LE, Pagliara S, Keyser UF, Jeney S, Lim RYH (2014). Selective transport control on molecular velcro made from intrinsically disordered proteins.
Nature Nanotechnology,
9(7), 525-530.
Abstract:
Selective transport control on molecular velcro made from intrinsically disordered proteins
The selectivity and speed of many biological transport processes transpire from a 'reduction of dimensionality' that confines diffusion to one or two dimensions instead of three. This behaviour remains highly sought after on polymeric surfaces as a means to expedite diffusional search processes in molecular engineered systems. Here, we have reconstituted the two-dimensional diffusion of colloidal particles on a molecular brush surface. The surface is composed of phenylalanine-glycine nucleoporins (FG Nups) - intrinsically disordered proteins that facilitate selective transport through nuclear pore complexes in eukaryotic cells. Local and ensemble-level experiments involving optical trapping using a photonic force microscope and particle tracking by video microscopy, respectively, reveal that 1-μm-sized colloidal particles bearing nuclear transport receptors called karyopherins can exhibit behaviour that varies from highly localized to unhindered two-dimensional diffusion. Particle diffusivity is controlled by varying the amount of free karyopherins in solution, which modulates the multivalency of Kap-binding sites within the molecular brush. We conclude that the FG Nups resemble stimuli-responsive molecular 'velcro', which can impart 'reduction of dimensionality' as a means of biomimetic transport control in artificial environments. © 2014 Macmillan Publishers Limited.
Abstract.
2013
Camposeo A, Greenfeld I, Tantussi F, Pagliara S, Moffa M, Fuso F, Allegrini M, Zussman E, Pisignano D (2013). Local mechanical properties of electrospun fibers correlate to their. internal nanostructure.
Camposeo A, Greenfeld I, Tantussi F, Pagliara S, Moffa M, Fuso F, Allegrini M, Zussman E, Pisignano D (2013). Local mechanical properties of electrospun fibers correlate to their internal nanostructure.
Nano Lett,
13(11), 5056-5062.
Abstract:
Local mechanical properties of electrospun fibers correlate to their internal nanostructure.
The properties of polymeric nanofibers can be tailored and enhanced by properly managing the structure of the polymer molecules at the nanoscale. Although electrospun polymer fibers are increasingly exploited in many technological applications, their internal nanostructure, determining their improved physical properties, is still poorly investigated and understood. Here, we unravel the internal structure of electrospun functional nanofibers made by prototype conjugated polymers. The unique features of near-field optical measurements are exploited to investigate the nanoscale spatial variation of the polymer density, evidencing the presence of a dense internal core embedded in a less dense polymeric shell. Interestingly, nanoscale mapping the fiber Young's modulus demonstrates that the dense core is stiffer than the polymeric, less dense shell. These findings are rationalized by developing a theoretical model and simulations of the polymer molecular structural evolution during the electrospinning process. This model predicts that the stretching of the polymer network induces a contraction of the network toward the jet center with a local increase of the polymer density, as observed in the solid structure. The found complex internal structure opens an interesting perspective for improving and tailoring the molecular morphology and multifunctional electronic and optical properties of polymer fibers.
Abstract.
Author URL.
Pagliara S, Schwall C, Keyser UF (2013). Optimizing diffusive transport through a synthetic membrane channel.
Adv Mater,
25(6), 844-849.
Author URL.
2012
Pagliara S, Polini A, Camposeo A, Schröder HC, Müller WEG, Pisignano D (2012). Electrical properties of in vitro biomineralized recombinant silicatein deposited by microfluidics.
Applied Physics Letters,
101(19).
Abstract:
Electrical properties of in vitro biomineralized recombinant silicatein deposited by microfluidics
We report the fabrication of silica dielectrics obtained by in vitro biomineralization of recombinant silicatein. We exploit pressure-driven microfluidics to deposit silicatein which catalyses the deposition of silica features with thickness in the range 2-6 μm. We follow the biomineralization process with staining and confocal fluorescence for an incubation time up to 5 days and correspondingly characterize the leakage current through the resulting biomineralized silica layer by embedding it into a metal-insulator-metal device. We further characterize the morphology of the biosilica surface through atomic force and scanning electron microscopy and demonstrate the electrical insulation within planar electrodes patterned over such surface with leakage currents in the pA range for applied bias up to tens of V. © 2012 American Institute of Physics.
Abstract.
Foderá V, Pagliara S, Otto O, Keyser UF, Donald AM (2012). Microfluidics reveals a flow-induced large-scale polymorphism of protein aggregates.
Journal of Physical Chemistry Letters,
3(19), 2803-2807.
Abstract:
Microfluidics reveals a flow-induced large-scale polymorphism of protein aggregates
Amyloid fibrils are characterized by a structural arrangement of cross β-sheet as a common motif. However they can also experience a more complicated packing into a variety of 3D supramolecular structures (polymorphism). Confinement and flow rate play a crucial role in protein aggregation in living systems, but controlling such parameters during in vitro experiments still remains an unsolved problem. Here we present evidence of the effect of flow rate on the aggregation process in a confined environment using microfluidics. Specifically, we show that a gradual transition from spherical aggregates, that is, spherulites, to thick fiber-like structures takes place as a result of increasing the flow rate. Such results have implications both for a basic understanding of the mechanism behind aggregation phenomena and in the development of novel biomaterials. © 2012 American Chemical Society.
Abstract.
Polini A, Pagliara S, Camposeo A, Cingolani R, Wang X, Schröder HC, Müller WEG, Pisignano D (2012). Optical properties of in-vitro biomineralised silica.
Sci Rep,
2Abstract:
Optical properties of in-vitro biomineralised silica.
Silicon is the second most common element on the Earth's crust and its oxide (SiO(2)) the most abundant mineral. Silica and silicates are widely used in medicine and industry as well as in micro- and nano-optics and electronics. However, the fabrication of glass fibres and components requires high temperature and non-physiological conditions, in contrast to biosilica structures in animals and plants. Here, we show for the first time the use of recombinant silicatein-α, the most abundant subunit of sponge proteins catalyzing biosilicification reactions, to direct the formation of optical waveguides in-vitro through soft microlithography. The artificial biosilica fibres mimic the natural sponge spicules, exhibiting refractive index values suitable for confinement of light within waveguides, with optical losses in the range of 5-10 cm(-1), suitable for application in lab-on-chips systems. This method extends biosilicification to the controlled fabrication of optical components by physiological processing conditions, hardly addressed by conventional technologies.
Abstract.
Author URL.
Lee CW, Pagliara S, Keyser U, Baumberg JJ (2012). Perpendicular coupling to in-plane photonics using arc waveguides fabricated via two-photon polymerization.
Applied Physics Letters,
100(17).
Abstract:
Perpendicular coupling to in-plane photonics using arc waveguides fabricated via two-photon polymerization
We demonstrate the concept of vertically standing arc waveguides to couple normally incident light into the plane of a photonic circuit or sensor array. The simple one-step direct write fabrication uses a low power picosecond microchip laser for two-photon polymerization with high-speed and low-cost. Arc waveguides with different arc radii and waveguide port diameters are obtained, with insertion loss down to 1.5 dB. This demonstration of a distinctly different architecture employing unsupported arc waveguides adds another dimension to photonic integration and opens up applications for environmental sensors, integrated microfluidics, bio-assay chips, as well as offering an alternate way of input/output-coupling to planar waveguides. © 2012 American Institute of Physics.
Abstract.
Ekpenyong AE, Whyte G, Chalut K, Pagliara S, Lautenschläger F, Fiddler C, Paschke S, Keyser UF, Chilvers ER, Guck J, et al (2012). Viscoelastic properties of differentiating blood cells are fate- and function-dependent.
PLoS One,
7(9).
Abstract:
Viscoelastic properties of differentiating blood cells are fate- and function-dependent.
Although cellular mechanical properties are known to alter during stem cell differentiation, understanding of the functional relevance of such alterations is incomplete. Here, we show that during the course of differentiation of human myeloid precursor cells into three different lineages, the cells alter their viscoelastic properties, measured using an optical stretcher, to suit their ultimate fate and function. Myeloid cells circulating in blood have to be advected through constrictions in blood vessels, engendering the need for compliance at short time-scales (minutes), compared to undifferentiated cells. These findings suggest that reduction in steady-state viscosity is a physiological adaptation for enhanced migration through tissues. Our results indicate that the material properties of cells define their function, can be used as a cell differentiation marker and could serve as target for novel therapies.
Abstract.
Author URL.
2011
Tu D, Pagliara S, Cingolani R, Pisignano D (2011). An electrospun fiber phototransistor by the conjugated polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylene-vinylene].
Applied Physics Letters,
98(2).
Abstract:
An electrospun fiber phototransistor by the conjugated polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylene-vinylene]
We investigate the photoresponse of field-effect transistors based on conjugated polymer electrospun fibers. The electrical performances of single fiber transistors are controlled by modulating the channel conductivity under white light illumination. We demonstrate a photoresponsivity up to 100 mA/W for a 500-nm channel width fiber phototransistor illuminated by an intensity of 9.6 mW/cm2. Studying the photoresponse switching cycles evidences that the photocurrent relaxation time can be reduced down to about 40 s by increasing the fiber surface-to-volume ratio. © 2011 American Institute of Physics.
Abstract.
Polini A, Pagliara S, Camposeo A, Biasco A, Schröder HC, Müller WEG, Pisignano D (2011). Biosilica electrically-insulating layers by soft lithography-assisted biomineralisation with recombinant silicatein.
Adv Mater,
23(40), 4674-4678.
Author URL.
Pagliara S, Chimerel C, Aarts DGAL, Langford R, Keyser UF (2011). Colloid flow control in microchannels and detection by laser scattering.
Progress in Colloid and Polymer Science,
139, 45-49.
Abstract:
Colloid flow control in microchannels and detection by laser scattering
We introduce a new approach towards the flow control and detection of colloids in microfluidic specimens. We fabricate hybrid polydimethylsiloxane (PDMS)/glass microfluidic chips equipped with parallel micrometer and sub-micrometer channels with different width and thickness. We image and detect the colloid flow direction through the microchannels by coupling laser-light-scattering in a restricted region of a single channel. We control single polymer colloids by means of a computerized pressure-based flow control system and study the Poiseuille flow through channels with different square cross section. We demonstrate the possibility of in situ sensing populations of colloids with different dimensions down to the sub-100 nm scale. © Springer-Verlag Berlin Heidelberg 2012.
Abstract.
Fodera V, Pagliara S, Keyser UF, Donald AM (2011). Flow-induced polymorphism of protein aggregates in micro channels.
Author URL.
Pagliara S, Vitiello MS, Camposeo A, Polini A, Cingolani R, Scamarcio G, Pisignano D (2011). Optical anisotropy in single light-emitting polymer nanofibers.
Journal of Physical Chemistry C,
115(42), 20399-20405.
Abstract:
Optical anisotropy in single light-emitting polymer nanofibers
We investigate the optical anisotropy of single nanofibers realized by electrospinning a conjugated polymer. Polarized infrared and micro-Raman measurements evidence a higher degree of molecular orientation in fibers processed from tetrahydrofuran solutions, with respect to samples spun from mixture with dimethyl sulfoxide. The fraction of ordered molecules is correlated to the fibers morphology. Polarized photoluminescence highlights a larger red shift (60 meV) for spectra from fibers processed from tetrahydrofuran, confirming the higher achieved molecular order resulting in reduced interchain separation and hence excitonic emission with lower transition energies compared to that from randomly aligned molecules. Conjugated polymer fibers are obtained, emitting light with polarization ratios up to 5, usable as polarized photonic nanosources. © 2011 American Chemical Society.
Abstract.
Pagliara S, Chimerel C, Langford R, Aarts DGAL, Keyser UF (2011). Parallel sub-micrometre channels with different dimensions for laser scattering detection.
Lab Chip,
11(19), 3365-3368.
Abstract:
Parallel sub-micrometre channels with different dimensions for laser scattering detection.
A novel and simple approach for the realization of polymer sub-micrometre channels is introduced by exploiting replica molding of Pt wires deposited by focused ion beam. We fabricate arrays of parallel channels with typical dimensions down to 600 nm and with variable height. We characterize the pressure-driven transport of polymer colloids through the channels in terms of the translocation frequency, amplitude and duration by implementing a laser scattering detection technique. We propose a prototype application of the presented platform such as the in situ sizing and sensing of populations of particles with different dimensions down to 50 nm.
Abstract.
Author URL.
Tu D, Pagliara S, Camposeo A, Potente G, Mele E, Cingolani R, Pisignano D (2011). Soft nanolithography by polymer fibers.
Advanced Functional Materials,
21(6), 1140-1145.
Abstract:
Soft nanolithography by polymer fibers
We report on the use of polymer fibers for large-area soft nanolithography on organic and inorganic surfaces with 50 nm resolution. The morphology of fibers and of the corresponding patterned gap is investigated, demonstrating a lateral dimension downscaling of up to nine times, which greatly increases the achieved resolution during pattern transfer. In this way, we realize polymer field effect transistors with channel length and width as low as 250 nm that are expected to show transistor transition frequency up to a few MHz, and are thus exploitable as low-cost radio-frequency identification devices. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Abstract.
2010
Polini A, Pagliara S, Stabile R, Netti GS, Roca L, Prattichizzo C, Gesualdo L, Cingolani R, Pisignano D (2010). Collagen-functionalised electrospun polymer fibers for bioengineering applications.
Soft Matter,
6(8), 1668-1674.
Abstract:
Collagen-functionalised electrospun polymer fibers for bioengineering applications
Polymer electrospun fibers are gaining increasing importance in nanobiotechnology, due to their intrinsic three-dimensional topography and biochemical flexibility. Here we present an in-depth study of protein functionalisation for polymethylmethacrylate fibers. We compare different coating approaches for type I collagen, including physisorption and covalent binding methods relying on functional linkers. The biofunctionalised fibers are investigated by scanning electron and confocal laser scanning microscopy, wettability measurements, Fourier-transform infrared spectroscopy, and protein quantification assays. We demonstrate that the largest amount of proteins adsorbed on fibers does not determine the best performance in terms of cell attachment and proliferation in vitro, which is instead related to the type of linking and the relevant role played by adsorption of serum biomolecules on the three-dimensional nanostructures. This study is relevant for designing and engineering novel biomaterials and scaffold architectures based on electrospun nanofibers. © 2010 the Royal Society of Chemistry.
Abstract.
Camposeo A, Pagliara S, Polini A, Pisignano D (2010). Conjugated polymer nanofibers: Novel light sources for microfluidic systems.
Optics InfoBase Conference PapersAbstract:
Conjugated polymer nanofibers: Novel light sources for microfluidic systems
We report on the fabrication of electrospun light-emitting polymer nanofibers made by conjugated and dye-doped polymers. The fibers exhibit diameter down to a few tens of nm, and emission in the visible and near-infrared spectral range. The investigation of the photoluminescence properties of the fibers evidences an emission mainly polarized along the fiber axis. The fibers are integrated in prototype microfluidic system as micro-scale polarized light sources. © 2009 Optical Society of America.
Abstract.
Camposeo A, Pagliara S, Polini A, Pisignano D (2010). Conjugated polymer nanofibers: Novel light sources for microfluidic systems.
Abstract:
Conjugated polymer nanofibers: Novel light sources for microfluidic systems
Abstract.
Pagliara S, Camposeo A, Mele E, Persano L, Cingolani R, Pisignano D (2010). Enhancement of light polarization from electrospun polymer fibers by room temperature nanoimprint lithography.
Nanotechnology,
21(21).
Abstract:
Enhancement of light polarization from electrospun polymer fibers by room temperature nanoimprint lithography.
We demonstrate the enhancement of the polarization ratio of light emitted from electrospun conjugated polymer nanofibers, by means of nanoimprint lithography carried out at room temperature. We provide evidence of tailoring the polarization properties by patterning light-emitting fibers at the nanoscale. The polarization ratios are increased up to a factor of 2.4 by gratings with periodicity (560 nm) matching the emission wavelength of the employed conjugated polymer. The use of room temperature nanoimprint lithography to pattern light-emitting polymer nanofibers represents a strategic route for realizing photonic crystals and distributed feedback polarized emitters on one-dimensional organic nanostructures.
Abstract.
Author URL.
Pagliara S, Camposeo A, Neves AAR, Polini A, Cingolani R, Pisignano D (2010). Integration of polarized light-emitting nanostructures for biomarker sensing. European Cells and Materials, 20(SUPPL.3).
Polini A, Pagliara S, Cingolani R, Pisignano D (2010). PMMA Electrospun Nanofibers for Scaffold Applications. Journal of Applied Biomaterials & Functional Materials, 8(2), 121-121.
Neves AAR, Camposeo A, Pagliara S, Saija R, Borghese F, Denti P, Iatì MA, Cingolani R, Maragò OM, Pisignano D, et al (2010). Rotational dynamics of optically trapped nanofibers.
Opt Express,
18(2), 822-830.
Abstract:
Rotational dynamics of optically trapped nanofibers.
We report on the experimental evidence of tilted polymer nanofiber rotation, using a highly focused linear polarized Gaussian beam. Torque is controlled by varying trapping power or fiber tilt angle. This suggests an alternative strategy to previously reported approaches for the rotation of nano-objects, to test fundamental theoretical aspects. We compare experimental rotation frequencies to calculations based on T-Matrix formalism, which accurately reproduces measured data, thus providing a comprehensive description of trapping and rotation dynamics of the linear nanostructures.
Abstract.
Author URL.
Tu D, Pagliara S, Camposeo A, Persano L, Cingolani R, Pisignano D (2010). Single light-emitting polymer nanofiber field-effect transistors.
Nanoscale,
2(10), 2217-2222.
Abstract:
Single light-emitting polymer nanofiber field-effect transistors.
We report on single nanofiber field-effect transistors made by the light-emitting polymer, poly(2-methoxy-5-(2-ethylhexoxy)-1,4-phenylenevinylene). We measure electrical performances comparable to or better than those of thin-film transistors by the same organic semiconductor, due to the molecular alignment induced by electrospinning, such as hole mobility of the order of 10(-3) cm(2) V(-1) s(-1) and on/off current ratios up to 780. In addition, we observe controllable photoluminescence intensity quenching by varying the gate voltage up to -40 V with device operation in the luministor mode. Single light-emitting polymer nanofiber transistors coupling electrical and optical functionalities open the way towards low cost and flexible one-dimensional switches and nanofiber-based light-emitting transistors.
Abstract.
Author URL.
Pagliara S, Camposeo A, Di Benedetto F, Polini A, Mele E, Persano L, Cingolani R, Pisignano D (2010). Study of optical properties of electrospun light-emitting polymer fibers.
Superlattices and Microstructures,
47(1), 145-149.
Abstract:
Study of optical properties of electrospun light-emitting polymer fibers
We realize light-emitting polymer fibers based on both optically inert polymers doped by molecules exhibiting optical gain and optically active conjugated polymers. Waveguiding properties of the produced polymer structures are demonstrated, with a loss coefficient of around 103 cm-1. We also find that single polymer fibers doped with gain molecules form Fabry-Pérot cavities, showing photoluminescence spectra with modes equally spaced by 1.7 nm. Coherent emission is demonstrated from fibers made upon increasing the excitation fluence above threshold values of the order of a few tens of μJ/cm2. © 2009 Elsevier Ltd. All rights reserved.
Abstract.
2009
Pagliara S, Camposeo A, Polini A, Cingolani R, Pisignano D (2009). Electrospun light-emitting nanofibers as excitation source in microfluidic devices.
Lab Chip,
9(19), 2851-2856.
Abstract:
Electrospun light-emitting nanofibers as excitation source in microfluidic devices.
We introduce the integration of organic, polarised light-emitting electrospun nanofibers and lab-on-a-chip microchannel geometries. The alignment and spinning electric field leads to ordered mesoscopic active areas, up to many mm(2), which exhibit polarised light emission and are fully compatible with microlithographies and microfluidics. We utilise the nanofibers demonstrating the photo-excitation of flowing dye chromophores in microchannels. This leads to easy decoupling the excitation and sample emission by polarisation analysers, thus remarkably increasing the imaging signal to background noise ratio.
Abstract.
Author URL.
Pagliara S, Camposeo A, Cingolani R, Pisignano D (2009). Hierarchical assembly of light-emitting polymer nanofibers in helical morphologies.
Applied Physics Letters,
95(26).
Abstract:
Hierarchical assembly of light-emitting polymer nanofibers in helical morphologies
Single electrospun nanofibers of light-emitting conjugated polymers hierarchically assemble at nano- to macroscopic lengthscales in various helical morphologies. At nanoscopic lengthscales, molecular chains follow the microscopic assembly, prevalently aligning along the fiber dynamic axis, as demonstrated by polarized photoluminescence spectroscopy. The role of molecular weight in the resulting assembling and optical properties is highlighted and discussed. Nanofibers based on the heaviest polymer exhibit the most stretched helical geometries and the highest suppression of the excitonic energy migration, resulting in the most blue-shifted photoluminescence with respect to thin films. © 2009 American Institute of Physics.
Abstract.
Neves AAR, Camposeo A, Pagliara S, Saija R, Borghese F, Denti P, Iati MA, Cingolani R, Marago OM, Pisignano D, et al (2009). Rotational dynamics of optically trapped polymeric nanofibers.
2008
Di Benedetto F, Camposeo A, Pagliara S, Mele E, Persano L, Stabile R, Cingolani R, Pisignano D (2008). Patterning of light-emitting conjugated polymer nanofibres.
Nat Nanotechnol,
3(10), 614-619.
Abstract:
Patterning of light-emitting conjugated polymer nanofibres.
Organic materials have revolutionized optoelectronics by their processability, flexibility and low cost, with application to light-emitting devices for full-colour screens, solar cells and lasers. Some low-dimensional organic semiconductor structures exhibit properties resembling those of inorganics, such as polarized emission and enhanced electroluminescence. One-dimensional metallic, III-V and II-VI nanostructures have also been the subject of intense investigation as building blocks for nanoelectronics and photonics. Given that one-dimensional polymer nanostructures, such as polymer nanofibres, are compatible with sub-micrometre patterning capability and electromagnetic confinement within subwavelength volumes, they can offer the benefits of organic light sources to nanoscale optics. Here we report on the optical properties of fully conjugated, electrospun polymer nanofibres. We assess their waveguiding performance and emission tuneability in the whole visible range. We demonstrate the enhancement of the fibre forward emission through imprinting periodic nanostructures using room-temperature nanoimprint lithography, and investigate the angular dispersion of differently polarized emitted light.
Abstract.
Author URL.
2007
Pagliara S, Persano L, Camposeo A, Cingolani R, Pisignano D (2007). Registration accuracy in multilevel soft lithography.
NANOTECHNOLOGY,
18(17).
Author URL.
Pagliara S, Persano L, Camposeo A, Cingolani R, Pisignano D (2007). Registration accuracy in multilevel soft lithography.
Nanotechnology,
18(17).
Abstract:
Registration accuracy in multilevel soft lithography
We investigate the registration accuracy achievable by multilevel soft lithography. By a specifically designed soft lithography aligner, we obtain, for the average misalignment between two registered patterned organic layers, values decreasing from (4.96 ± 0.02) to (0.50 ± 0.01) μm upon increasing the Young's modulus of the stamp materials from 1.8 to 2600 MPa. This clearly identifies in the stamp distortions the main factor limiting the registration accuracy. The potentiality to achieve registration within 500 nm over areas of 50 × 50 μm2 is demonstrated, opening the way for soft lithographies with high overlay alignment accuracy. © IOP Publishing Ltd.
Abstract.
