Gabriel Gomila - Academia.edu (original) (raw)

Papers by Gabriel Gomila

The AlgZR system controls ribonucleotide reduction on mucoid and non-mucoid biofilms and links it to oxidative stress

Electrical Properties of Outer Membrane Extensions from Shewanella Oneidensis MR-1

Nanoscale, 2021

Shewanella oneidensis MR-1 are metal-reducing bacterial cells able to exchange electrons with sol... more Shewanella oneidensis MR-1 are metal-reducing bacterial cells able to exchange electrons with solid-phase minerals outside the cell. These bacterial cells can produce outer membrane extensions (OMEs) that are tens of...

Dielectric nanotomography based on electrostatic force microscopy: A numerical analysis

Journal of Applied Physics, 2020

Electrostatic force microscopy (EFM) can image nanoscale objects buried below the surface. Here, ... more Electrostatic force microscopy (EFM) can image nanoscale objects buried below the surface. Here, we theoretically show that this capability can be used to obtain nanotomographic information, i.e., the physical dimensions and dielectric properties, of buried nano-objects. These results constitute a first step toward implementing a nondestructive dielectric nanotomography technique based on EFM with applications in materials sciences and life sciences.

Biosensors and Bioelectronics, 2019

Organic Electronic Materials offer an untapped potential for novel tools for low-invasive electro... more Organic Electronic Materials offer an untapped potential for novel tools for low-invasive electrophysiological recording and stimulation devices. Such materials combine semiconducting properties with tailored surface chemistry, elastic mechanical properties and chemical stability in water. In this work, we investigated solution processed Electrolyte Gated Organic Field Effect Transistors (EGOFETs) based on a small molecule semiconductor. We demonstrate that EGOFETs based on a blend of soluble organic semiconductor 2,8-Difluoro-5,11-bis(triethylsilylethynyl)anthradithiophene (diF-TES-ADT) combined with an insulating polymer show excellent sensitivity and long-term recording under electrophysiological applications. Our devices can stably record the extracellular potential of human pluripotent 2 stem cell derived cardiomyocyte cells (hPSCs-CMs) for several weeks. In addition, cytotoxicity tests of pharmaceutical drugs, such as Norepinephrine and Verapamil was achieved with excellent sensitivity. This work demonstrates that organic transistors based on organic blends are excellent bioelectronics transducer for extracellular electrical recording of excitable cells and tissues thus providing a valid alternative to electrochemical transistors.

Mapping the dielectric constant of a single bacterial cell at the nanoscale with scanning dielectric force volume microscopy

Nanoscale, 2019

A method to map the dielectric constant of non-planar samples is presented, and applied to single... more A method to map the dielectric constant of non-planar samples is presented, and applied to single bacterial cells.

Scientific Reports, 2017

Ribonucleotide reductases (RNR) catalyze the last step of deoxyribonucleotide synthesis, and are ... more Ribonucleotide reductases (RNR) catalyze the last step of deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. Three forms of RNR exist: classes I, II, and III. While eukaryotic cells use only class Ia RNR, bacteria can harbor any combination of classes, granting them adaptability. The opportunistic pathogen Pseudomonas aeruginosa surprisingly encodes all three classes, allowing it to thrive in different environments. Here we study an aspect of the complex RNR regulation whose molecular mechanism has never been elucidated, the well-described induction through oxidative stress, and link it to the AlgZR two-component system, the primary regulator of the mucoid phenotype. Through bioinformatics, we identify AlgR binding locations in RNR promoters, which we characterize functionally through EMSA and physically through AFM imaging. Gene reporter assays in different growth models are used to study the AlgZR-mediated control on the RNR network under various environmental conditions and physiological states. Thereby, we show that the two-component system AlgZR, which is crucial for bacterial conversion to the mucoid phenotype associated with chronic disease, controls the RNR network and directs how the DNA synthesis pathway is modulated in mucoid and non-mucoid biofilms, allowing it to respond to oxidative stress. Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium, but it can also be a dangerous and adaptable opportunistic pathogen. In particular, it is known to cause severe chronic lung infections in immunocompromised patients and other at-risk groups. In cystic fibrosis (CF) patients, this infection is associated with a poor prognosis, leading to severely impaired lung function and an increased risk of respiratory failure, and is the primary cause of morbidity and mortality 1. P. aeruginosa initially colonizes the CF lung in a non-mucoid form (characterized by non-detectable alginate production and causing an asymptomatic infection). However, at later stages of lung colonization, P. aeruginosa switches its phenotype to a mucoid alginate-overproducer variant, leading to rapid pulmonary deterioration 2,3. Alginate production protects P. aeruginosa from phagocytosis, antibiotic penetration, and desiccation 4,5 , but it is also an energy-intensive process and is therefore closely regulated and activated only when a chronic infection reaches a critical point. It involves a large number of enzymes and precursor substrates. Of particular relevance is the algD (and consecutive genes) operon, encoding the main enzymes for alginate production, and the algC gene from the algC-argB operon, a multifunctional enzyme required for several pathways including alginate biosynthesis and LPS production 6. These genes are controlled by products of the algU/mucABCD operon; their transcription is directed by the alternative sigma factor AlgU (sigma E), which is commonly sequestered by the anti-sigma factor MucA. It has been reported that several types of cellular stress can induce proteolytic degradation of MucA, releasing AlgU and transiently activating alginate synthesis 7 , but the stable mucoid phenotype is generated through the selection of mutations in the regulatory genes, usually in mucA 8,9. Apart from the algD and algC operons, the AlgU sigma factor regulates the transcription of the fimS(alg-Z)-algR operon, which encodes the AlgZR two-component system 10,11. In this system, FimS is the membrane

To Be or not to Be a Source of Shot Noise: an Open Problem of Generation Recombination Noise

AIP Conference Proceedings, 2003

We address the fundamental question wether generation recombination noise can transform into shot... more We address the fundamental question wether generation recombination noise can transform into shot noise at increasing values of the applied bias (current or voltage). From the seminal work of Van Vliet and Fassett (1965) the analytical answer to this question is affirmative. By contrast, recent numerical results by Bonani and Ghione (1999) provided a negative answer. For a simple semiconductor two level model consisting of a conducting band and an impurity level which provides charge carriers we solve exactly the appropriate second order stochastic differential equation self-consistently coupled with the Poisson solver. The effect of the diffusion current, neglected in the first analytical approach, is found to inhibit the cross-over between generation-recombination and shot noise, thus confirming more recent numerical results. Open problems related to the microscopic interpretation of these new results are pointed out.

Stochastic Resonance in Noisy Nondynamical Systems

Physical Review Letters, 1998

Noise Properties of Ballistic Exclusions

Noise in Physical Systems and 1/f Fluctuations - ICNF 2001 - Proceedings of the 16th International Conference, 2001

Nanosensors based on biological olfactory receptors

Quartz tuning fork-based conductive atomic force microscope with glue-free solid metallic tips

Sensors and Actuators A: Physical, 2015

ABSTRACT Here we devise a conductive Atomic Force Microscope (C-AFM) based on quartz tuning forks... more ABSTRACT Here we devise a conductive Atomic Force Microscope (C-AFM) based on quartz tuning forks (QTFs) and metallic tips capable of simultaneously imaging the topography and conductance of a sample with nanoscale spatial resolution. The system is based on a header design which allows the metallic tip to be placed in tight and stable mechanical contact with the QTF without the need to use any glue. This allows electrical measurements to be taken with an electrically excited QTF with the two prongs free. The amplitude oscillation of the QTF is used to control the tip–sample distance and to acquire the topographic images. Meanwhile, the metallic tip is connected to a current–voltage amplifier circuit to measure the tip–sample field emission/tunnelling current and to produce the conductive images. This method allows decoupled electrical measurement of the topography and electrical properties of the sample. The results we obtain from calibration samples demonstrate the feasibility of this measurement method and the adequacy of the performance of the system.

Ultramicroscopy, Jan 10, 2015

With the use of the atomic force microscope (AFM), the Nanomicrobiology field has advanced drasti... more With the use of the atomic force microscope (AFM), the Nanomicrobiology field has advanced drastically. Due to the complexity of imaging living bacterial processes in their natural growing environments, improvements have come to a standstill. Here we show the in situ nanoscale imaging of the growth and division of single bacterial cells on planar substrates with the atomic force microscope. To achieve this, we minimized the lateral shear forces responsible for the detachment of weakly adsorbed bacteria on planar substrates with the use of the so called dynamic jumping mode with very soft cantilever probes. With this approach, gentle imaging conditions can be maintained for long periods of time, enabling the continuous imaging of the bacterial cell growth and division, even on planar substrates. Present results offer the possibility to observe living processes of untrapped bacteria weakly attached to planar substrates.

Artificial nose integrating biological olfactory receptors and NEMS

Shot Noise in Macroscopic Resistors: A Predicted Experimental Evidence?

Noise in Physical Systems and 1/F Fluctuations, 2001

Small scale structures: the fabrication of polymeric nanostructures for biomedical applications using pattern replication techniques

Contributions to …, 2005

Diffusion-controlled deposition of natural nanovesicles containing G-protein coupled receptors for biosensing platforms

Soft Matter, 2012

The role of boundary conditions in shot noise in elastic diffusive conductors

Semiconductor Science and Technology, 2000

ABSTRACT The role played by boundary conditions at a kinetic level in determining the noise prope... more ABSTRACT The role played by boundary conditions at a kinetic level in determining the noise properties of mesoscopic diffusive conductors is evaluated by decomposing the current fluctuations, into fluctuations of boundaries, self-consistent electric potential and the intrinsic Langevin source. We show that the self-consistent contribution is essentially controlled by the range of energies determined by the distribution function at the contacts together with the differential conductivity in energy space. The intrinsic contribution is completely determined by the boundary conditions and is expressed in closed analytical form in these terms. The present formulation provides a unifying microscopic approach of the noise properties of mesoscopic diffusive conductors showing that (i) in the absence of Coulomb interaction the Fano factor γ takes values bounded in the range (1/3)≤γ≤1 and (ii) in the presence of Coulomb interaction the values of γ are no longer bounded in the above range and enhanced shot noise becomes possible.

Physica B: Condensed Matter, 2002

We study the effects of dimensionality on the noise properties of perfect ballistic conductors wi... more We study the effects of dimensionality on the noise properties of perfect ballistic conductors with carriers satisfying fractional exclusion statistics (FES). We show that under non-degenerate conditions noise properties are independent of dimensionality as well as of carrier statistics. In contrast, under strongly degenerate conditions noise properties depend on dimensionality, but not on carrier statistics. Interestingly, under weakly degenerate conditions noise properties depend on both dimensionality and carrier statistics. In this last case, the effects of carrier statistics are more pronounced for low dimensional systems, thus suggesting that one-dimensional systems are the most appropriate to experimentally investigate the properties of FES.

Microfluidics and Nanofluidics, 2013

Here we describe a high-throughput impedance flow cytometer on a chip. This device was built usin... more Here we describe a high-throughput impedance flow cytometer on a chip. This device was built using compact and inexpensive electronic instrumentation. The system was used to count and size a mixed cell sample containing red blood cells and white blood cells. It demonstrated a counting capacity of up to *500 counts/s and was validated through a synchronised high-speed optical detection system. In addition, the device showed excellent discrimination performance under high-throughput conditions. Keywords Microcytometry Á Microfluidics Á Impedance Á Electronics Á Red blood cells (RBCs) Á White blood cells (WBCs)

Effects of interface states on the non-stationary transport properties of Schottky contacts and metal-insulator-semiconductor tunnel diodes

Journal of Physics D: Applied Physics, 1999

... The parameters are the same as those in figure 2. with the fraction of interface states in eq... more ... The parameters are the same as those in figure 2. with the fraction of interface states in equilibrium with the metal, Ca lf , in equation (13). Moreover, we may set Dsa ≈ 0 in equation (A3) and take Dsb ≈ Ds. Hence, the admittance for this range of bias can be rewritten as ...