by Keyword: Channel

Nauryzgaliyeva, Z, Corredera, IG, Garreta, E, Montserrat, N, (2023). Harnessing mechanobiology for kidney organoid research Frontiers In Cell And Developmental Biology 11, 1273923

Recently, organoids have emerged as revolutionizing tools with the unprecedented potential to recreate organ-specific microanatomy in vitro. Upon their derivation from human pluripotent stem cells (hPSCs), organoids reveal the blueprints of human organogenesis, further allowing the faithful recapitulation of their physiology. Nevertheless, along with the evolution of this field, advanced research exposed the organoids' shortcomings, particularly regarding poor reproducibility rates and overall immatureness. To resolve these challenges, many studies have started to underscore the relevance of mechanical cues as a relevant source to induce and externally control hPSCs differentiation. Indeed, established organoid generation protocols from hPSCs have mainly relyed on the biochemical induction of fundamental signalling pathways present during kidney formation in mammals, whereas mechanical cues have largely been unexplored. This review aims to discuss the pertinence of (bio) physical cues within hPSCs-derived organoid cultures, while deciphering their effect on morphogenesis. Moreover, we will explore state-of-the-art mechanobiology techniques as revolutionizing means for understanding the underlying role of mechanical forces in biological processes in organoid model systems.

JTD Keywords: development, hpscs, mechanobiology, nephrogenesis, Activated ion-channel, Development, Extracellular-matrix viscoelasticity, Forces, Hpscs, Ips cells, Mechanical regulation, Mechanobiology, Nephrogenesis, Nephron progenitors, Organoids, Pluripotent stem-cells, Self-renewal, Substrate mechanics, Tissue

Bodrenko, I, Ceccarelli, M, Acosta-Gutierrez, S, (2023). The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics Physical Chemistry Chemical Physics 25, 26497-26506

General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores. General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. In the diffusive transport process of molecules, electrostatic interactions can help to decrease the entropic free energy barrier.

JTD Keywords: Channel, Diffusion barrier, Electric-field, Molecular-dynamics, Outer-membrane permeability, Permeation, Porins, Simulations, Translocation, Transport

Qi, C, Gutierrez, SS, Lavriha, P, Othman, A, Lopez-Pigozzi, D, Bayraktar, E, Schuster, D, Picotti, P, Zamboni, N, Bortolozzi, M, Gervasio, FL, Korkhov, VM, (2023). Structure of the connexin-43 gap junction channel in a putative closed state Elife 12, RP87616

Gap junction channels (GJCs) mediate intercellular communication by connecting two neighbouring cells and enabling direct exchange of ions and small molecules. Cell coupling via connexin-43 (Cx43) GJCs is important in a wide range of cellular processes in health and disease (Churko and Laird, 2013; Liang et al., 2020; Poelzing and Rosenbaum, 2004), yet the structural basis of Cx43 function and regulation has not been determined until now. Here, we describe the structure of a human Cx43 GJC solved by cryo-EM and single particle analysis at 2.26 Å resolution. The pore region of Cx43 GJC features several lipid-like densities per Cx43 monomer, located close to a putative lateral access site at the monomer boundary. We found a previously undescribed conformation on the cytosolic side of the pore, formed by the N-terminal domain and the transmembrane helix 2 of Cx43 and stabilized by a small molecule. Structures of the Cx43 GJC and hemichannels (HCs) in nanodiscs reveal a similar gate arrangement. The features of the Cx43 GJC and HC cryo-EM maps and the channel properties revealed by molecular dynamics simulations suggest that the captured states of Cx43 are consistent with a closed state.© 2023, Qi, Acosta Gutierrez et al.

JTD Keywords: cryo-em, dehydroepiandrosterone dhea, expression, gap junction channel, gene, gja1 mutations, hemichannel, membrane protein, phenotype, protein, structure, system, visualization, Biochemistry, Chemical biology, Connexin-43, Cryo-em, Gap junction channel, Hemichannel, Human, Membrane protein, Molecular biophysics, Oculodentodigital dysplasia, Structural biology, Structure

Claudia, GM, Ivan, G, Laia, OM, Emilio, JP, Maria-Pau, G, Maurizio, V, Luis, CJ, Marta, P, (2023). Influence of ECAP process on mechanical, corrosion and bacterial properties of Zn-2Ag alloy for wound closure devices Materials & Design 228, 111817

Actual polymeric wound closure devices are not optimal for load-bearing applications due to the low mechanical properties and the risk of inflammation and bacterial infection mainly produced by multifil-ament and braided configurations. Biodegradable metallic Zn alloys are promising materials candidates; however, mechanical performance, corrosion behaviour, and biological response should be controlled in order to inhibit the risk of inflammation and bacterial infection. To this end, a Zn-2Ag (2 wt% Ag) alloy was processed by ECAP to evaluate the concurrent combined effect of grain refinement and Ag alloying on biodegradation and antibacterial activity. Two ECAP cycles were successfully applied to a Zn-2Ag alloy obtaining a homogeneous ultra-fine-grained structure in which nanoindentation maps suggested isotro-pic mechanical properties. Lower UTS and YS with higher elongation was reported after ECAP with similar corrosion rates as before processing. ECAP processed samples showed a homogeneous Ag+ release below the minimum inhibitory concentration for S. Aureus and no antibacterial effect was observed by diffusion. As expected, the presence of Ag in Zn-Ag alloys reduced bacterial attachment. Nevertheless, ECAP processed Zn-2Ag provided an excellent antibacterial activity after 3 h probably caused by the uniformly degraded and thus, non- stable, surface observed after bacterial adhesion.(c) 2023 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (

JTD Keywords: Behavior, Binary alloys, Biodegradable zinc-alloys, Biomaterials, Equal channel angular pressing, Grain-refinement, In-vitro degradation, Mg, Microstructure, Nanoindentation, Progress, Staphylococcus-aureus, Temperature superplasticity, Ultrafine-grained materials, Zinc alloys, Zn alloys

Castagna, R, Kolarski, D, Durand-de Cuttoli, R, Maleeva, G, (2022). Orthogonal Control of Neuronal Circuits and Behavior Using Photopharmacology Journal Of Molecular Neuroscience 72, 1433-1442

Over the last decades, photopharmacology has gone far beyond its proof-of-concept stage to become a bona fide approach to study neural systems in vivo. Indeed, photopharmacological control has expanded over a wide range of endogenous targets, such as receptors, ion channels, transporters, kinases, lipids, and DNA transcription processes. In this review, we provide an overview of the recent progresses in the in vivo photopharmacological control of neuronal circuits and behavior. In particular, the use of small aquatic animals for the in vivo screening of photopharmacological compounds, the recent advances in optical modulation of complex behaviors in mice, and the development of adjacent techniques for light and drug delivery in vivo are described.

JTD Keywords: brain circuits, circadian rhythm, in vivo photomodulation, in vivo technology, neuronal receptors, Architecture, Azobenzene photoswitches, Brain circuits, Channels, Circadian rhythm, In vivo photomodulation, In vivo technology, Light, Modulator, Neuronal receptors, Optical control, Optogenetics, Pharmacology, Photopharmacology, Receptors, Systems

Sierra-Agudelo, J, Rodriguez-Trujillo, R, Samitier, J, (2022). Microfluidics for the Isolation and Detection of Circulating Tumor Cells Microfluidics And Biosensors In Cancer Research 1379, 389-412

Nowadays, liquid biopsy represents one of the most promising techniques for early diagnosis, monitoring, and therapy screening of cancer. This novel methodology includes, among other techniques, the isolation, capture, and analysis of circulating tumor cells (CTCs). Nonetheless, the identification of CTC from whole blood is challenging due to their extremely low concentration (1-100 per ml of whole blood), and traditional methods result insufficient in terms of purity, recovery, throughput and/or viability of the processed sample. In this context, the development of microfluidic devices for detecting and isolating CTCs offers a wide range of new opportunities due to their excellent properties for cell manipulation and the advantages to integrate and bring different laboratory processes into the microscale improving the sensitivity, portability, reducing cost and time. This chapter explores current and recent microfluidic approaches that have been developed for the analysis and detection of CTCs, which involve cell capture methods based on affinity binding and label-free methods and detection based on electrical, chemical, and optical sensors. All the exposed technologies seek to overcome the limitations of commercial systems for the analysis and isolation of CTCs, as well as to provide extended analysis that will allow the development of novel and more efficient diagnostic tools.© 2022. The Author(s), under exclusive license to Springer Nature Switzerland AG.

JTD Keywords: cancer detection, cancer diagnosis, cancer-cells, capture, chip, circulating tumor cells, enrichment, liquid biopsy, microchannel, separation, ultra-fast, Cancer detection, Cancer diagnosis, Circulating tumor cells, Label-free isolation, Liquid biopsy, Microfluidics

Yang, BQ, Wang, YX, Vorobii, M, Sauter, E, Koenig, M, Kumar, R, Rodriguez-Emmenegger, C, Hirtz, M, (2022). Evaluation of Dibenzocyclooctyne and Bicyclononyne Click Reaction on Azido-Functionalized Antifouling Polymer Brushes via Microspotting Advanced Materials Interfaces 9, 2102325

Garrido-Charles, A, Huet, A, Matera, C, Thirumalai, A, Hernando, J, Llebaria, A, Moser, T, Gorostiza, P, (2022). Fast Photoswitchable Molecular Prosthetics Control Neuronal Activity in the Cochlea Journal Of The American Chemical Society 144, 9229-9239

Artificial control of neuronal activity enables the study of neural circuits and restoration of neural functions. Direct, rapid, and sustained photocontrol of intact neurons could overcome the limitations of established electrical stimulation such as poor selectivity. We have developed fast photoswitchable ligands of glutamate receptors (GluRs) to enable neuronal control in the auditory system. The new photoswitchable ligands induced photocurrents in untransfected neurons upon covalently tethering to endogenous GluRs and activating them reversibly with visible light pulses of a few milliseconds. As a proof of concept of these molecular prostheses, we applied them to the ultrafast synapses of auditory neurons of the cochlea that encode sound and provide auditory input to the brain. This drug-based method afforded the optical stimulation of auditory neurons of adult gerbils at hundreds of hertz without genetic manipulation that would be required for their optogenetic control. This indicates that the new photoswitchable ligands are also applicable to the spatiotemporal control of fast spiking interneurons in the brain.

JTD Keywords: Acid, Azobenzene, Glutamate-receptor, Ion channels, Mechanisms, Nerve, Optical switches, Release, Stimulation

Puiggalí-Jou, A, Molina, BG, Lopes-Rodrigues, M, Michaux, C, Perpète, EA, Zanuy, D, Aleman, C, (2021). Self-standing, conducting and capacitive biomimetic hybrid nanomembranes for selective molecular ion separation Physical Chemistry Chemical Physics 23, 16157-16164

Hybrid free-standing biomimetic materials are developed by integrating the VDAC36 β-barrel protein into robust and flexible three-layered polymer nanomembranes. The first and third layers are prepared by spin-coating a mixture of poly(lactic acid) (PLA) and poly(vinyl alcohol) (PVA). PVA nanofeatures are transformed into controlled nanoperforations by solvent-etching. The two nanoperforated PLA layers are separated by an electroactive layer, which is successfully electropolymerized by introducing a conducting sacrificial substrate under the first PLA nanosheet. Finally, the nanomaterial is consolidated by immobilizing the VDAC36 protein, active as an ion channel, into the nanoperforations of the upper layer. The integration of the protein causes a significant reduction of the material resistance, which decreases from 21.9 to 3.9 kΩ cm2. Electrochemical impedance spectroscopy studies using inorganic ions and molecular metabolites (i.e.l-lysine and ATP) not only reveal that the hybrid films behave as electrochemical supercapacitors but also indicate the most appropriate conditions to obtain selective responses against molecular ions as a function of their charge. The combination of polymers and proteins is promising for the development of new devices for engineering, biotechnological and biomedical applications.

JTD Keywords: channels, evolution, filter, Outer-membrane proteins

Comelles, J., Hortigüela, V., Samitier, J., Martinez, E., (2012). Versatile gradients of covalently bound proteins on microstructured substrates Langmuir 28, (38), 13688-13697

In this work, we propose an easy method to produce highly tunable gradients of covalently bound proteins on topographically modified poly(methyl methacrylate). We used a rnicrofluidic approach to obtain linear gradients with high slope (0.5, relevant at the single-cell level. These protein gradients were characterized using fluorescence microscopy and surface plasmon resonance. Both experimental results and theoretical modeling on the protein gradients generated have proved them to be highly reproducible, stable up to 7 days, and easily tunable. This method enables formation of versatile cell culture platforms combining both complex biochemical and physical cues in an attempt to approach in vitro cell culture methods to in vivo cellular microenvironments.

JTD Keywords: Cell-migration, Microfluidic channel, Surface, Streptavidin, Molecules, Topography, Mechanisms, Generation, Responses, Guidance

Darwish-, N., Caballero, D., Moreno, M., Errachid, A., Samitier, J., (2010). Multi-analytic grating coupler biosensor for differential binding analysis Sensors and Actuators B: Chemical 144, (2), 413-417

In this paper, a multiple-channel extension of a dual-grating Coupler biosensor is presented as a Solution for the problem of resolving different selectivities, Usual when heterogeneous samples are analyzed. Several differently functionalized channels can perform quantitative analysis of competiting recognition events, Suppress shifts due to buffer changes and even monitorize drifts coming from the light Source. Here, the multiple-channel approach is developed and proven for a four-channel configuration, providing a resolution limit of 10(-5) Refractive index Units (RIU) and with an a potentially Unlimited scalability. Finally, a differential HSA recognition event is monitored, at both an IgG functionalized channel and at a blocked one.

JTD Keywords: Optical grating coupler, Multi-channel biorecognition, On-chip reference

Mesquita, J., Fiz, J. A., Solà, J., Morera, J., Jané, R., (2010). Regular and non regular snore features as markers of SAHS Engineering in Medicine and Biology Society (EMBC) 32nd Annual International Conference of the IEEE , IEEE (Buenos Aires, Argentina) , 6138-6141

Sleep Apnea-Hypopnea Syndrome (SAHS) diagnosis is still done with an overnight multi-channel polysomnography. Several efforts are being made to study profoundly the snore mechanism and discover how it can provide an opportunity to diagnose the disease. This work introduces the concept of regular snores, defined as the ones produced in consecutive respiratory cycles, since they are produced in a regular way, without interruptions. We applied 2 thresholds (TH/sub adaptive/ and TH/sub median/) to the time interval between successive snores of 34 subjects in order to select regular snores from the whole all-night snore sequence. Afterwards, we studied the effectiveness that parameters, such as time interval between successive snores and the mean intensity of snores, have on distinguishing between different levels of SAHS severity (AHI (Apnea-Hypopnea Index)<5h/sup -1/, AHI<10 h/sup -1/, AHI<15h/sup -1/, AHI<30h/sup -1/). Results showed that TH/sub adaptive/ outperformed TH/sub median/ on selecting regular snores. Moreover, the outcome achieved with non-regular snores intensity features suggests that these carry key information on SAHS severity.

JTD Keywords: Practical, Experimental/ acoustic signal processing, Bioacoustics, Biomedical measurement, Diseases, Feature extraction, Medical signal processing, Patient diagnosis, Pneumodynamics, Sleep/ nonregular snore features, SAHS markers, Sleep apnea hypopnea syndrome, Overnight multichannel polysomnography, Snore mechanism

Nussio, M. R., Oncins, G., Ridelis, I., Szili, E., Shapter, J. G., Sanz, F., Voelcker, N. H., (2009). Nanomechanical characterization of phospholipid bilayer islands on flat and porous substrates: A force spectroscopy study Journal of Physical Chemistry B , 113, (30), 10339-10347

In this study, we compare for the first time the nanomechanical properties of lipid bilayer islands on flat and porous surfaces. 1,2-Dimyzistoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) bilayers were deposited on flat (silicon and mica) and porous silicon (pSi) substrate surfaces and examined using atomic force spectroscopy and force volume imaging. Force spectroscopy measurements revealed the effects of the underlying substrate and of the lipid phase on the nanomechanical properties of bilayers islands. For mica and silicon, significant differences in breakthrough force between the center and the edges of bilayer islands were observed for both phospolipids. These differences were more pronounced for DMPC than for DPPC, presumably due to melting effects at the edges of DMPC bilayers. In contrast, bilayer islands deposited on pSi yielded similar breakthrough forces in the central region and along the perimeter of the islands, and those values in turn were similar to those measured along the perimeter of bilayer islands deposited on the flat substrates. The study also demonstrates that pSi is suitable solid support for the formation of pore-spanning phospholipid bilayers with potential applications in transmembrane protein studies, drug delivery, and biosensing.

JTD Keywords: Black lipid-membranes, Gold surfaces, Supported bilayers, Channel activity, Micro-BLMS, Silicon, Proteins, Vesicles, AFM, Temperature measurement

Gorostiza, P., Isacoff, E. Y., (2008). Optical switches for remote and noninvasive control of cell signaling Science 322, (5900), 395-399

Although the identity and interactions of signaling proteins have been studied in great detail, the complexity of signaling networks cannot be fully understood without elucidating the timing and location of activity of individual proteins. To do this, one needs a means for detecting and controlling specific signaling events. An attractive approach is to use light, both to report on and control signaling proteins in cells, because light can probe cells in real time with minimal damage. Although optical detection of signaling events has been successful for some time, the development of the means for optical control has accelerated only recently. Of particular interest is the development of chemically engineered proteins that are directly sensitive to light.

JTD Keywords: Ion channels, Acetylcholine receptor, Glutamate-receptor, Potassium channel, K+ channel, Light, Neurons, Channelrhodopsin-2, Manipulation, Activation