Live-cell Experiments Research Articles

γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells.

Connecting two small molecules, such as ligands, fluorophores, or lipids, together via a linker with amide bonds is a widely used strategy to generate synthetic bifunctional molecules for various biological and biomedical applications. Such bifunctional molecules have been used in live-cell experiments under the assumption that they should be stable in cells. However, we recently found that a membrane-targeting bifunctional molecule, composed of a lipopeptide and the small-molecule ligand trimethoprim, referred to as mgcTMP, underwent amide-bond cleavage in mammalian cells. In this work, we first identified γ-secretase as the major protease degrading mgcTMP in cells. We next investigated the intracellular degradation of several different types of amide-linked bifunctional compounds and found that N-terminally fatty acid-conjugated small molecules are susceptible to γ-secretase-mediated amide-bond cleavage. In contrast, amide-linked bifunctional molecules composed of two small molecules, such as ligands and hydrophobic groups, which lack lipid modification, did not undergo intracellular degradation. These findings highlight a previously overlooked consideration for the development and application of lipid-based bifunctional molecules in chemical biology research.

Promiscuous Janus kinase binding to cytokine receptors modulates signaling efficiencies and contributes to cytokine pleiotropy.

Janus kinases (JAKs) bind to class I and II cytokine receptors, activating signaling and regulating gene transcription through signal transducer and activator of transcription (STAT) proteins. Type I interferons (IFNs) require the JAK members TYK2 and JAK1, which bind to the receptor subunits IFNAR1 and IFNAR2, respectively. We investigated the role of JAKs in regulating IFNAR signaling activity. Synthetic IFNARs in which the extracellular domains of IFNAR1 and IFNAR2 are replaced with nanobodies had near-native type I IFN signaling, whereas the homomeric variant of IFNAR2 initiated much weaker signaling, despite harboring docking sites for JAKs and STATs. Cells with JAK1 and TYK2 knockout (KO) showed residual signaling, suggesting partial complementation by the remaining JAKs, particularly when they were overexpressed. Live-cell micropatterning experiments confirmed the promiscuous binding of JAK1, JAK2, and TYK2 to IFNAR1 and IFNAR2, and their recruitment correlated with their relative cellular abundances. However, each JAK had a different efficacy in inducing cross-phosphorylation and downstream signaling. JAK binding was also promiscuous for other cytokine receptors, including IFN-L1, IL-10Rβ, TPOR, and GHR, but not for EPOR, which activated different downstream signaling pathways. These findings suggest that competitive binding of JAKs to cytokine receptors together with the varying absolute and relative abundances of the JAKs in different cell types can account for the cell type-dependent signaling pleiotropy of cytokine receptors.

Near-Infrared Ratiometric Hemicyanine Fluorescent Probes for Monitoring Mitochondrial pH Dynamics in Live Cells during Oxidative Stress and Hypoxia.

Novel near-infrared ratiometric molecules (probes A and B) produced by linking formyl-functionalized xanthene and methoxybenzene moieties, respectively, onto a xanthene-hemicyanine framework are detailed. Probe A exhibited a primary absorption peak at 780 nm and a shoulder peak at 730 nm and exhibited fluorescence at 740 nm↓ (signifies a downward shift in intensity upon acidification) in a pH 9.3 buffer and 780 nm↑ at pH 2.8 under excitation at 700 nm. Probe B featured absorptions at 618 and 668 nm at pH 3.2 and at 717 nm at pH 8.6, and fluorescence at 693 nm↑ at pH 3.2 and at 739 nm↓ at pH 8.6, in mostly the red to near-IR region. The ratiometric changes in the intensity of the fluorescent absorptions were reversed between A and B upon acidification as indicated by the arrows. Theoretical calculations confirmed that there were slight changes in conformation between probes and the protonated molecules, suggesting that the changes in emission spectra were due mostly to conjugation effects. Calculations at the APFD/6-311+g(d,p) level with a solvent described by the polarizable continuum model resulted in pK a values for A at 6.33 and B at 6.41, in good agreement with the experimentally determined value of 6.97 and an average of 6.40, respectively. The versatilities of the probes were demonstrated in various experimental contexts, including the effective detection of mitochondrial pH fluctuations. Live cell experiments involving exposure to different pH buffers in the presence of H+ ionophores, monitoring mitophagy processes during cell starvation, studying hypoxia induced by CoCl2 treatment, and investigating responses to various oxidative stresses are detailed. Our findings highlight the potential of attaching xanthene and methoxybenzaldehyde groups onto xanthene-hemicyanine structures as versatile tools for monitoring pH changes in a variety of cellular environments and processes.

Membrane tension evolution and mechanical regulation of melittin-induced membrane poration

Abstract Membrane tension plays a crucial role in various fundamental cellular processes, with one notable example being the T cell-mediated elimination of tumor cells through perforin-induced membrane perforation by amplifying cellular force. However, the mechanisms governing the regulation of biomolecular activities at the cell interface by membrane tension remain elusive. In this study, we investigated the correlation between membrane tension and poration activity of melittin, a prototypical pore-forming peptide, using dynamic giant unilamellar vesicle leakage assays combined with flickering tension analysis, molecular dynamics simulations, and live cell assays. The results demonstrate that an increase in membrane tension enhances the activity of melittin, particularly near its critical pore-forming concentration. Moreover, peptide actions such as binding, insertion, and aggregation in the membrane further influence the evolution of membrane tension. Live cell experiments reveal that artificially enhancing membrane tension effectively enhances melittin’s ability to induce pore formation and disrupt membranes, resulting in up to a ten-fold increase in A549 cell mortality when exposed to a concentration of 2.0-μg⋅mL−1 melittin. Our findings elucidate the relationship between membrane tension and the mechanism of action as well as pore-forming efficiency of melittin, while providing a practical mechanical approach for regulating functional activity of molecules at the cell-membrane interface.

Intracellular Protein Editing to Enable Incorporation of Non-Canonical Residues into Endogenous Proteins.

The ability to study proteins in a cellular context is crucial to our understanding of biology. Here, we report a new technology for "intracellular protein editing", drawing from intein- mediated protein splicing, genetic code expansion, and endogenous protein tagging. This protein editing approach enables us to rapidly and site specifically install residues and chemical handles into a protein of interest. We demonstrate the power of this protein editing platform to edit cellular proteins, inserting epitope peptides, protein-specific sequences, and non-canonical amino acids (ncAAs). Importantly, we employ an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented here will be applied to a diverse set of problems, enabling novel experiments in live mammalian cells and therefore provide unique biological insights.

The use of slime molds as a design guide in urban design, A case of Turkey/İzmir/Karabağlar

Urban design is a complex and challenging process that encompasses many disciplines, such as urban planning, architecture, and landscape. On the urban design scale, it’s important to consider short paths compatible with pedestrian behaviors, especially in public spaces, in terms of designing healthier and more accessible urban areas. But conventional design processes, which are mostly based on the designer’s observations or intuitions, fail to satisfy user behaviors in usage. Studies reveal that P. polycephalum slime molds have the potential to guide good urban planning. However, it is noteworthy that there are not enough studies yet in the disciplines of architecture and urban design on the design of pedestrian ways in small-scale areas, and there is a need for research. In this direction, this study is the first step of a method that is aimed at being developed for the disciplines of architecture and urban design in the long process. The main hypothesis is that a design template can be created as a result of graphical analysis of living slime mold experiments on the map, especially in undesigned empty urban areas, for architects and planners, and it can provide creative suggestions to the designer. In this direction, in this study, a graphic design template proposal was created based on live cell experiments at a site in Izmir, Turkey, which the local government aims to design as a pedestrianized zone and open for competition. Slime molds are used directly as a computer rather than as inspiration for a computer, and a pedestrian-oriented design template proposal develops with the behavioral models of slime molds. Compared to the award-winning designs developed for the same area, it has been shown that even within the framework of simple graphical measurements, it gives better results and creates more optimal routes on main and side roads. It is envisaged that this study can play a pioneering role for studies involving more detailed mathematical models that can begin in the field of architecture and urban design.

Development of an Azobenzene-Based Cell Culture Photoresponsive Platform for In Situ Modulation of Surface Topography in Wet Environments.

Azopolymers are light-responsive materials that hold promise to transform in vitro cell culture systems. Through precise light illumination, they facilitate substrate pattern formation and erasure, allowing for the dynamic control and creation of active interfaces between cells and materials. However, these materials exhibit a tendency to locally detach from the supporting glass in the presence of aqueous solutions, such as cell culture media, due to the formation of blisters, which are liquid-filled cavities generated at the azopolymer film-glass interface. These blisters impede precise structurization of the surface of the azomaterial, limiting their usage for surface photoactivation in the presence of cells. In this study, we present a cost-effective and easily implementable method to improve the azopolymer-glass interface stability through silane functionalization of the glass substrate. This method proved to be efficient in preventing blister formation, thereby enabling the dynamic modulation of the azopolymer surface in situ for live-cell experiments. Furthermore, we proved that the light-illumination conditions used to induce azopolymer surface variations do not induce phototoxic effects. Consequently, this approach facilitates the development of a photoswitchable azopolymer cell culture platform for studying the impact of multiple in situ inscription and erasure cycles on cell functions while maintaining a physiological wet microenvironment.

Essential role of N-terminal SAM regions in STIM1 multimerization and function

The single-pass transmembrane protein Stromal Interaction Molecule 1 (STIM1), located in the endoplasmic reticulum (ER) membrane, possesses two main functions: It senses the ER-Ca2+ concentration and directly binds to the store-operated Ca2+ channel Orai1 for its activation when Ca2+ recedes. At high resting ER-Ca2+ concentration, the ER-luminal STIM1 domain is kept monomeric but undergoes di/multimerization once stores are depleted. Luminal STIM1 multimerization is essential to unleash the STIM C-terminal binding site for Orai1 channels. However, structural basis of the luminal association sites has so far been elusive. Here, we employed molecular dynamics (MD) simulations and identified two essential di/multimerization segments, the α7 and the adjacent region near the α9-helix in the sterile alpha motif (SAM) domain. Based on MD results, we targeted the two STIM1 SAM domains by engineering point mutations. These mutations interfered with higher-order multimerization of ER-luminal fragments in biochemical assays and puncta formation in live-cell experiments upon Ca2+ store depletion. The STIM1 multimerization impeded mutants significantly reduced Ca2+ entry via Orai1, decreasing the Ca2+ oscillation frequency as well as store-operated Ca2+ entry. Combination of the ER-luminal STIM1 multimerization mutations with gain of function mutations and coexpression of Orai1 partially ameliorated functional defects. Our data point to a hydrophobicity-driven binding within the ER-luminal STIM1 multimer that needs to switch between resting monomeric and activated multimeric state. Altogether, these data reveal that interactions between SAM domains of STIM1 monomers are critical for multimerization and activation of the protein.

A bioluminescent probe for imaging human cytochrome P450 2J2 activity in vitro and in vivo

Human Cytochrome P450 2J2 (CYP 2J2) is closely associated with various physiological diseases. However, bioluminescence (BL) tools for monitoring CYP 2J2 activity have not yet been reported. Herein, we rationally designed a BL probe, PJ-Luc, capable of real-time imaging of CYP 2J2. In vitro studies demonstrated that PJ-Luc can effectively respond to exogenous CYP 2J2 with high selectivity and a low detection limit (LOD = 0.11 nM). Further, living cell experiments indicated that PJ-Luc can accurately quantify the ratio of endogenous CYP 2J2 amounts in HepG-2-Luc and A549-Luc cells. Moreover, an ultrahigh BL signal-to-noise ratio (S/N = 2.3×105) was achieved in tumor-bearing mouse models. These results suggest that PJ-Luc has great potential in the diagnosis of tumors and other CYP-2J2-related diseases.

Silicon-Rhodamine Functionalized Evocalcet Probes Potently and Selectively Label Calcium Sensing Receptors In Vitro, In Vivo, and Ex Vivo.

The calcium sensing receptor (CaSR) is a ubiquitously expressed G-protein coupled receptor (GPCR) that regulates extracellular calcium signals via the parathyroid glands. CaSR has recently also been implicated in noncalcitropic pathophysiologies like asthma, gut inflammation, and cancer. To date, molecular tools that enable the bioimaging of CaSR in tissues are lacking. Based on in silico analyses of available structure-activity relationship data on CaSR ligands, we designed and prepared silicon-rhodamine (SiR) conjugates of the clinically approved drug evocalcet. The new probes EvoSiR4 and EvoSiR6, with differing linker lengths at the evocalcet carboxyl end, both showed a 6-fold and 3-fold increase in potency toward CaSR (EC50 < 45 nM) compared to evocalcet and the evocalcet-linker conjugate, respectively, in an FLIPR-based cellular functional assay. The specificity of the EvoSiR probes toward CaSR binding and the impact of albumin was evaluated in live cell experiments. Both probes showed strong albumin binding, which facilitated the clearance of nonspecific binding interactions. Accordingly, in zebrafish embryos, EvoSiR4 specifically labeled the high CaSR expressing neuromasts of the lateral line in vivo. EvoSiR4 was also assessed in human parathyroid tissues ex vivo, showing a specific absolute CaSR-associated fluorescence compared to that of parathyroid autofluorescence. In summary, functionalization of evocalcet by SiR led to the preparation of potent and specific fluorescent CaSR probes. EvoSiR4 is a versatile small-molecular probe that can be employed in CaSR-related biomedical analyses where antibodies are not applicable.

Interplay of condensation and chromatin binding underlies BRD4 targeting.

Nuclear compartments form via biomolecular phase separation, mediated through multivalent properties of biomolecules concentrated within condensates. Certain compartments are associated with specific chromatin regions, including transcriptional initiation condensates, which are composed of transcription factors and transcriptional machinery, and form at acetylated regions including enhancer and promoter loci. While protein self-interactions, especially within low-complexity and intrinsically disordered regions, are known to mediate condensation, the role of substrate-binding interactions in regulating the formation and function of biomolecular condensates is underexplored. Here, utilizing live-cell experiments in parallel with coarse-grained simulations, we investigate how chromatin interaction of the transcriptional activator BRD4 modulates its condensate formation. We find that both kinetic and thermodynamic properties of BRD4 condensation are affected by chromatin binding: nucleation rate is sensitive to BRD4-chromatin interactions, providing an explanation for the selective formation of BRD4 condensates at acetylated chromatin regions, and thermodynamically, multivalent acetylated chromatin sites provide a platform for BRD4 clustering below the concentration required for off-chromatin condensation. This provides a molecular and physical explanation of the relationship between nuclear condensates and epigenetically modified chromatin that results in their mutual spatiotemporal regulation, suggesting that epigenetic modulation is an important mechanism by which the cell targets transcriptional condensates to specific chromatin loci.

Cyclopropenes as Chemical Reporters for Dual Bioorthogonal and Orthogonal Metabolic Labeling of DNA.

Dual bioorthogonal labeling enables the investigation and understanding of interactions in the biological environment that are not accessible by a single label. However, applying two bioorthogonal reactions in the same environment remains challenging due to cross-reactivity. We developed a pair of differently modified 2'-deoxynucleosides that solved this issue for dual and orthogonal labeling of DNA. Inverse-electron demand Diels-Alder and photoclick reactions were combined to attach two different fluorogenic labels to genomic DNA in cells. Using a small synthetic library of 1- and 3-methylcyclopropenyl-modified 2'-deoxynucleosides, two 2'-deoxyuridines were identified to be the fastest-reacting ones for each of the two bioorthogonal reactions. Their orthogonal reactivity could be evidenced in vitro. Primer extension experiments were performed with both 2'-deoxyuridines investigating their replication properties as substitutes for thymidine and evaluating subsequent labeling reactions on the DNA level. Finally, dual, orthogonal and metabolic fluorescent labeling of genomic DNA was demonstrated in HeLa cells. An experimental procedure was developed combining intracellular transport and metabolic DNA incorporation of the two 2'-deoxyuridines with the subsequent dual bioorthogonal labeling using a fluorogenic cyanine-styryl tetrazine and a fluorogenic pyrene-tetrazole. These results are fundamental for advanced metabolic labeling strategies for nucleic acids in the future, especially for live cell experiments.

Cyclopropene als Chemische Reporter für die Duale Bioorthogonale und Orthogonale Metabolische Markierung von DNA

AbstractDie duale bioorthogonale Markierung ermöglicht die Untersuchung und das Verständnis von Wechselwirkungen in der biologischen Umgebung, die mit einer einzigen Markierung nicht zugänglich sind. Eine Herausforderung bleibt jedoch die Anwendung von zwei bioorthogonalen Reaktionen in der gleichen Umgebung aufgrund von Kreuzreaktivität. Um dieses Problem für die duale und orthogonale Markierung von DNA zu lösen, haben wir zwei unterschiedlich modifizierte 2′‐Desoxynukleoside entwickelt. Mit Hilfe der Diels‐Alder‐Reaktion mit inversem Elektronenbedarf und Photoklick‐Reaktion wurde genomische DNA in Zellen mit zwei verschiedenen fluorogenen Markern verknüpft. Aus einer kleinen synthetischen Bibliothek aus 1‐ und 3‐methylcyclopropenyl‐modifizierten 2′‐Desoxynukleosiden wurden zwei 2′‐Desoxyuridine identifiziert, die am schnellsten in jeweils einer der beiden bioorthogonalen Reaktionen reagieren. Ihre orthogonale Reaktivität konnte in vitro nachgewiesen werden. Ihre Replikationseigenschaften als Ersatz für Thymidin wurden in Primerverlängerungsexperimenten untersucht, um die anschließenden Markierungsreaktionen an DNA abzuschätzen. Schließlich wurde eine duale, orthogonale und metabolische Fluoreszenzmarkierung von genomischer DNA in HeLa‐Zellen nachgewiesen. Es wurde ein experimentelles Protokoll entwickelt, das den intrazellulären Transport und den metabolischen DNA‐Einbau der beiden 2′‐Desoxyuridine mit der anschließenden dualen bioorthogonalen Markierung unter Verwendung eines fluorogenen Cyanin‐Styryl‐Tetrazins und eines fluorogenen Pyren‐Tetrazols kombiniert. Diese Ergebnisse sind von grundlegender Bedeutung für fortgeschrittene metabolische Markierungsstrategien für Nukleinsäuren in der Zukunft, insbesondere in lebenden Zellen.

Mechanistic differences between linear vs. spirocyclic dialkyldiazirine probes for photoaffinity labeling.

Dialkyldiazirines have emerged as a photo-reactive group of choice for interactome mapping in live cell experiments. Upon irradiation, 'linear' dialkyldiazirines produce dialkylcarbenes which are susceptible to both intramolecular reactions and unimolecular elimination processes, as well as diazoalkanes, which also participate in intermolecular labeling. Cyclobutylidene has a nonclassical bonding structure and is stable enough to be captured in bimolecular reactions. Cyclobutanediazirines have more recently been studied as photoaffinity probes based on cyclobutylidene, but the mechanism, especially with respect to the role of putative diazo intermediates, was not fully understood. Here, we show that photolysis (365 nm) of cyclobutanediazirines can produce cyclobutylidene intermediates as evidenced by formation of their expected bimolecular and unimolecular products, including methylenecyclopropane derivatives. Unlike linear diazirines, cyclobutanediazirine photolysis in the presence of tetramethylethylene produces a [2 + 1] cycloaddition adduct. By contrast, linear diazirines produce diazo compounds upon low temperature photolysis in THF, whereas diazo compounds are not detected in similar photolyses of cyclobutanediazirines. Diazocyclobutane, prepared by independent synthesis, is labile, reactive toward water and capable of protein alkylation. The rate of diazocyclobutane decomposition is not affected by 365 nm light, suggesting that the photochemical conversion of diazocyclobutane to cyclobutylidene is not an important pathway. Finally, chemical proteomic studies revealed that a likely consequence of this primary conversion to a highly reactive carbene is a marked decrease in labeling by cyclobutanediazirine-based probes relative to linear diazirine counterparts both at the individual protein and proteome-wide levels. Collectively, these observations are consistent with a mechanistic picture for cyclobutanediazirine photolysis that involves carbene chemistry with minimal formation of diazo intermediates, and contrasts with the photolyses of linear diazirines where alkylation by diazo intermediates plays a more significant role.

Biochemical features of the Cry4B toxin of Bacillus thuringiensis subsp. israelensis and its interaction with BT-R3, a bitopic cadherin G-protein coupled receptor in Anopheles gambiae.

The cadherin G-protein coupled receptor BT-R3 in the mosquito Anopheles gambiae is a single membrane-spanning α-helical (bitopic) protein that represents the most abundant and functionally diverse group of membrane proteins. Binding of the Cry4B toxin of Bacillus thuringiensis subsp. israelensis (Bti) to BT-R3 triggers a Mg2+-dependent signalling pathway in the mosquito that involves stimulation of G protein α-subunit, which subsequently launches a coordinated signalling cascade involving Na+/K+-ATPase. Described in this study is the behaviour of the Cry4B purified active protein toxin in solution relative to its protoxin predecessor produced by Bti as well as identification of the region within BT-R3 of An. gambiae to which the toxin binds. The relationship and behaviour of protoxin and toxin were ascertained in vitro by solubility studies in an alkaline environment like that of the mosquito larval midgut. To identify the specific toxin-binding site within BT-R3, the full-length coding sequence of the bt-r3 gene was amplified and cloned in pENTR/D-TOTO and subcloned in pXINSECT-DEST38 resulting in recombinant pXINSECT-DEST38-bt-r3. Cytotoxicity was analysed using Trichoplusia ni High Five™ insect cells transfected with the pXINSECT-DEST38-bt-r3 plasmid rendering them susceptible to the Cry4B toxin. Truncation mutational analyses, receptor-toxin binding studies and live cell experiments were used to elucidate the toxin-binding site in BT-R3. The N-terminal half of the Cry4B protoxin was cleaved releasing active Cry4B toxin. The nontoxic C-terminal portion was degraded into small peptide fragments. The receptor BT-R3 contained a single toxin-binding site--a 106-amino acid polypeptide bounded by Ile1359 and Ser1464 (1359IS1464) localized in the 11th cadherin repeat of the receptor. The structural features of the toxin-binding site are critical to the specificity, selectivity and affinity of the active toxin and for the design and development of novel Bti-based biopesticides.

Probing the metalloproteome: an 8-mercaptoquinoline motif enriches minichromosome maintenance complex components as significant metalloprotein targets in live cells.

Affinity-based probes are valuable tools for detecting binding interactions between small molecules and proteins in complex biological environments. Metalloproteins are a class of therapeutically significant biomolecules which bind metal ions as part of key structural or catalytic domains and are compelling targets for study. However, there is currently a limited range of chemical tools suitable for profiling the metalloproteome. Here, we describe the preparation and application of a novel, photoactivatable affinity-based probe for detection of a subset of previously challenging to engage metalloproteins. The probe, bearing an 8-mercaptoquinoline metal chelator, was anticipated to engage several zinc metalloproteins, including the 26S-proteasome subunit Rpn11. Upon translation of the labelling experiment to mammalian cell lysate and live cell experiments, proteomic analysis revealed that several metalloproteins were competitively enriched. The diazirine probe SMK-24 was found to effectively enrich multiple components of the minichromosome maintenance complex, a zinc metalloprotein assembly with helicase activity essential to DNA replication. Cell cycle analysis experiments revealed that HEK293 cells treated with SMK-24 experienced stalling in G0/G1 phase, consistent with inactivation of the DNA helicase complex. This work represents an important contribution to the library of cell-permeable chemical tools for studying a collection of metalloproteins for which no previous probe existed.

Photovoltage transient technique: an alternative approach to real-time analysis of membrane interface dynamic processes

&lt;sec&gt;The dynamic interactions between active molecules and the cell membrane play a crucial role in various fundamental biological processes. The photovoltage transient technique developed in recent years has provided an &lt;i&gt;in situ&lt;/i&gt;, real-time, and non-invasive approach to studying dynamic processes at the membrane interface. In this technique, the photoelectric response of silicon wafers is used to generate charges and record voltage transient pulses in the charging and discharging process of phospholipid membranes. These pulses directly reflect the instantaneous structure and properties of the membrane. By analyzing the temporal evolution of voltage pulses, the dynamic changes in membrane structure induced by molecular actions can be elucidated. In particular, this technique provides valuable insights into the timing of transitions between different functional states. In this paper, the working principle, equipment setup, and data processing methods used in photovoltage transient analysis are comprehensively reviewed. Furthermore, the use of supported phospholipid bilayers as model cell membranes highlights recent progress of this technique in investigating the mechanisms underlying membrane interactions of active molecules such as surfactants, polymers, peptides, and nanoparticles. Finally, its advantages and limitations are evaluated, and its development prospects are discussed.&lt;/sec&gt;&lt;sec&gt;The photovoltage transient technique is initially used to analyze the charging and discharging curves, as well as the hydration process, of single- and multi-layered membranes composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) phospholipids. Previously, X-ray diffraction (XRD) and quartz crystal microbalance with dissipation (QCM-D) technology were commonly utilized for the real-time monitoring of the swelling process in phospholipid membranes, providing the information about changes in mass and thickness of &lt;i&gt;Z&lt;/i&gt;-direction layers. In contrast, the photovoltage transient technique presents additional insights into the kinetics of the swelling process and timing of transitions between different stages. The present study demonstrates the effectiveness of photovoltage transient technique in real-time monitoring of membrane interface processes, specifically, it quantitatively measures the characteristic &lt;i&gt;τ&lt;/i&gt; value of DOPC phospholipid membrane, thereby enabling further development of quantitative analysis method for this technique. Then, the photovoltage transient technique, in conjunction with giant unilamellar vesicle (GUV) leakage assays, atomic force microscopy (AFM) and QCM-D, is employed to monitor the structural perturbation of surfactants (TTAB) and polymers (Brij35 and PVPk30) on the membranes. Specifically, Brij35 primarily undergoes an adsorption-accumulation-penetration process; whereas PVPk30 exhibits a dynamic equilibrium between molecular adsorption-desorption and/or membrane permeation-healing competing mechanisms. This disparity in membrane action processes elucidates the discrepancy observed in their cytotoxicity during live cell experiments. The ability of photovoltage transient technology to investigate the entire membrane as a research subject along with its high sensitivity enables it to capture fluctuations in data points that reflect the coexistence of competitive mechanisms. Furthermore, photovoltage monitoring reveals the occurrence of peptide-induced membrane permeabilization. The distinct mechanism of action on the membrane between melittin (as a representative antimicrobial peptide) and TAT (a typical cell penetrating peptide) is elucidated. Finally, the conductive carbon dots (CDs) induced phenomena of membrane overcharging and overdischarging, are likely to be attributed to charge transfer between the silicon substrate and the embedded conductive CDs.&lt;/sec&gt;

Development and Evaluation of Biochips Specialized for Cell Counting

Cell counters, which are dedicated cell analyzers, can be used to analyze cellular status. Cell counters are smaller and less expensive (about $13,000) than other cell analysis devices such as flow cytometers (FACS), real-time PCR, and sequencers, and can discriminate between life and death of fluorescently stained cells. Cell death can be roughly divided into two types: apoptosis and necrosis, but Cell counters cannot distinguish between apoptosis and necrosis in cells. This study developed a biochip system for inexpensive, simple, and capable of distinguishing between live, apoptotic, and necrotic cells. This biochip system (70 x 150 x 80 mm) comprises a slide into which fluorescently stained cells are injected, an LED light source, and a camera system. When cells stained with a fluorescent reagent are irradiated at the excitation wavelength, they fluoresce. By changing the combination of fluorescent reagent and excitation wavelength, live, apoptotic, and necrotic cells can be photographed. Then they are processed by a cell counting program using existing methods to determine numbers of live, dead, and necrotic cells. To demonstrate the effectiveness of this system, we conducted live cell, apoptosis, and necrosis detection experiments using colon cancer cells. Results of each experiment using the biochip system were compared with visual cell counts made by an operator. The novel biochip system successfully distinguishes between live, apoptotic and necrotic cells. Detection time was &lt;1 s, and the detection error was 9%, compared to visual inspection.

Facilitating focussed proton radiation of single cells by automated cell targeting and novel design of live cell chamber

Targeted radiation of single cells with focussed sub-micron ion beams enables unique investigations in advanced high resolution radiobiology research. Since 2018, the Centre for Ion Beam Applications (CIBA) has operated a dedicated live-cell beam line to study radiobiology on single cells. Recently, we have upgraded this radiobiology beam line with enhanced precision in dose delivery and beam alignment by installing a beam blanking system and stage-mounted exit nozzle, respectively. We have increased efficiency of cell targeting through process automation, combined with exploiting a machine-learning algorithm, Cellpose, for rapid cell recognition to produce a fully automated cell targeting functionality with accurate cell identification. Concordant with further streamlining of our experimental workflows, here we describe the “cell slide”, our novel live-cell chamber assembly, which simplifies and drastically improves throughput and turn-around time in live-cell experiments. Cell slide has been specifically developed to support live-cell radiobiology applications on microbeam platforms.

Transcription Factor Dynamics: One Molecule at a Time.

Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.