Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe.

Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with inactive chromatin. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single living cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during 4-day differentiation, namely on the first and third days, whereas nearly no changes occurred on the second and fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscapes), which combines genetically encoded epigenetic probes and machine learning approaches, enables classification of multiparametric epigenetic signatures of single cells during stem cell differentiation and potentially in other biological models.

Harmonizing Energies: The Interplay Between a Nonplanar SalEn-Type Molecule and a TEMPO Moiety in a New Hybrid Energy-Storing Redox-Conducting Polymer.

Redox-conducting polymers based on SalEn-type complexes have attracted considerable attention due to their potential applications in electrochemical devices. However, their charge transfer mechanisms, physical and electrochemical properties remain unclear, hindering their rational design and optimization. This study aims to establish the influence of monomer geometry on the polymer's properties by investigating the properties of novel nonplanar SalEn-type complexes, poly[N,N'-bis(salicylidene)propylene-2-(hydroxy)diaminonickel(II)], and its analog with 2,2,6,6-tetramethylpiperidinyl-N-oxyl (TEMPO)-substituted bridge (MTS). To elucidate the charge transfer mechanism, operando UV-Vis spectroelectrochemical analysis, electrochemical impedance spectroscopy, and electron paramagnetic resonance are employed. Introducing TEMPO into the bridge moiety enhanced the specific capacity of the poly(MTS) material to 95 mA h g-1, attributed to TEMPO's and conductive backbone's charge storage capabilities. Replacement of the ethylenediimino-bridge with a 1,3-propylenediimino- bridge induced significant changes in the complex geometry and material's morphology, electrochemical, and spectral properties. At nearly the same potential, polaron and bipolaron particles emerged, suggesting intriguing features at the overlap point of the electroactivity potentials ranges of polaron-bipolaron and TEMPO, such as a disruption in the connection between TEMPO and the conjugation chain or intramolecular charge transfer. These results offer valuable insights for optimizing strategies to create organic materials with tailored properties for use in catalysis and battery applications.

Thermodynamic model for voltammetric responses in conducting redox polymers.

Electroactive polymer materials are known to play important roles in a vast spectrum of modern applications such as in supercapacitors, fuel cells, batteries, medicine, and smart materials, etc. They are usually divided into two main groups: first, conducting π-conjugated organic polymers, which conduct electricity by cation-radicals delocalized over a polymer chain; second, redox polymers, which conduct electricity via an electron-hopping mechanism. Polymer materials belonging to these two main groups have been thoroughly studied and their thermodynamic and kinetic models have been built. However, in recent decades a lot of mixed-type materials have been discovered and investigated. To the best of our knowledge, a thermodynamic-based description of conducting redox polymers (CRPs) has not been provided yet. In this work, we present a thermodynamic model for voltammetric responses of conducting redox polymers. The derived model allows one to extract thermodynamic parameters of a CRP including the polaron delocalization degree and redox active groups interaction constant. The model was verified with voltammetric experiments on three recently synthesized CRPs and showed a satisfactory predictive ability. The simulated data are in good agreement with the experiment. We believe that developing theoretical descriptions for CRPs and other types of electroactive materials with the ability to simulate their electrochemical responses may help in future realization of new systems with superior characteristics for electrochemical energy storage, chemical sensors, pharmacological applications, etc.

Tuning the Charge Transport in Nickel Salicylaldimine Polymers by the Ligand Structure.

The conductivity of the polymeric energy storage materials is the key factor limiting their performance. Conductivity of polymeric NiSalen materials, a prospective class of energy storage materials, was found to depend strongly on the length of the bridge between the nitrogen atoms of the ligand. Polymers obtained from the complexes containing C3 alkyl and hydroxyalkyl bridges showed an electrical conductivity one order of magnitude lower than those derived from more common complexes with C2 alkyl bridges. The observed difference was studied by means of cyclic voltammetry on interdigitated electrodes and operando spectroelectrochemistry, combined with density functional theory (DFT) calculations.

Signatures of Dermal Fibroblasts from RDEB Pediatric Patients.

The recessive form of dystrophic epidermolysis bullosa (RDEB) is a debilitating disease caused by impairments in the junctions of the dermis and the basement membrane of the epidermis. Mutations in the COL7A1 gene induce multiple abnormalities, including chronic inflammation and profibrotic changes in the skin. However, the correlations between the specific mutations in COL7A1 and their phenotypic output remain largely unexplored. The mutations in the COL7A1 gene, described here, were found in the DEB register. Among them, two homozygous mutations and two cases of compound heterozygous mutations were identified. We created the panel of primary patient-specific RDEB fibroblast lines (FEB) and compared it with control fibroblasts from healthy donors (FHC). The set of morphological features and the contraction capacity of the cells distinguished FEB from FHC. We also report the relationships between the mutations and several phenotypic traits of the FEB. Based on the analysis of the available RNA-seq data of RDEB fibroblasts, we performed an RT-qPCR gene expression analysis of our cell lines, confirming the differential status of multiple genes while uncovering the new ones. We anticipate that our panels of cell lines will be useful not only for studying RDEB signatures but also for investigating the overall mechanisms involved in disease progression.

Novel homogeneous photocatalyst for oxygen to hydrogen peroxide reduction in aqueous media.

An isoquinolinium-pyrrole donor-acceptor dyad was found to exhibit photocatalytic activity in oxygen-to-peroxide photoreduction with oxalate as a sacrificial electron donor. The concentration of hydrogen peroxide was shown to reach a plateau of 0.57 mM. The screening of related pyridinium-pyrrole dyads showed the importance of the isoquinoline moiety in securing the photocatalytic activity.

Diastereospecific and Highly Site-Selective Functionalization of C70 Fullerene by a Reaction with Diethyl N-Arylaziridine-2,3-dicarboxylates.

The diastereospecific and highly site-selective cycloaddition of N-arylazomethine ylides generated in situ from diethyl N-arylaziridine-2,3-dicarboxylates to C70 fullerene is reported. The reaction provides C70 fulleropyrrolidines in up to hundreds on a milligram scale as α- and ß-adducts in a 4:1 ratio with a controlled stereochemical outcome: cis-aziridines give exclusively trans-adducts, and trans-aziridines give only cis-adducts. The 1H and 13C{1H} NMR spectra for different isomeric adducts were recorded and analyzed to identify some characteristic features, which permit an easy identification of isomeric adducts of this type.

Optimization of Sulfonated Polycatechol:PEDOT Energy Storage Performance by the Morphology Control.

Anionic catechol-containing polymers represent a promising class of functional dopants for the capacity improvement of conductive polymers. For example, sulfonated poly(vinylcatechol) SPVC with outstanding theoretical capacity was used as a dopant for poly(ethylenedixythiophene) (PEDOT) conductive polymer, increasing its energy storage performance. However, such materials suffer from insufficient utilization of the theoretical capacity of SPVC originating from non-optimal morphology. In the present study, we performed systematic optimization of the composition and morphology of the PEDOT:SPVC material as a function of the deposition parameters to overcome this problem. As a result, a capacity of 95 mAh·g-1 was achieved in a thin film demonstrating considerable electrochemical stability: 75% capacity retention after 100 cycles and 57% after 1000 cycles. Since the capacity was found to suffer from thickness limitation, a nanocomposite of PEDOT:SPVC and single-walled carbon nanotubes with high PEDOT:SPVC loading was fabricated, yielding the capacitance 178 F·g-1 or 89 F·cm-2. The capacity values exceed non-optimized film twofold for thin film and 1.33 times for nanocomposite with carbon nanotubes. The obtained results demonstrate the importance of fine-tuning of the composition and morphology of the PEDOT:SPVC materials to ensure optimal interactions between the redox/anionic and conductive components.

Accounting for B-cell Behavior and Sampling Bias Predicts Anti-PD-L1 Response in Bladder Cancer.

Cancer immunotherapy is predominantly based on T cell-centric approaches. At the same time, the adaptive immune response in the tumor environment also includes clonally produced immunoglobulins and clonal effector/memory B cells that participate in antigen-specific decisions through their interactions with T cells. Here, we investigated the role of infiltrating B cells in bladder cancer via patient dataset analysis of intratumoral immunoglobulin repertoires. We showed that the IgG1/IgA ratio is a prognostic indicator for several subtypes of bladder cancer and for the whole IMVigor210 anti-PD-L1 immunotherapy study cohort. A high IgG1/IgA ratio associated with the prominence of a cytotoxic gene signature, T-cell receptor signaling, and IL21-mediated signaling. Immunoglobulin repertoire analysis indicated that effector B-cell function, rather than clonally produced antibodies, was involved in antitumor responses. From the T-cell side, we normalized a cytotoxic signature against the extent of immune cell infiltration to neutralize the artificial sampling-based variability in immune gene expression. Resulting metrics reflected proportion of cytotoxic cells among tumor-infiltrating immune cells and improved prediction of anti-PD-L1 responses. At the same time, the IgG1/IgA ratio remained an independent prognostic factor. Integration of the B-cell, natural killer cell, and T-cell signatures allowed for the most accurate prediction of anti-PD-L1 therapy responses. On the basis of these findings, we developed a predictor called PRedIctive MolecUlar Signature (PRIMUS), which outperformed PD-L1 expression scores and known gene signatures. Overall, PRIMUS allows for reliable identification of responders among patients with muscle-invasive urothelial carcinoma, including the subcohort with the low-infiltrated "desert" tumor phenotype.

Resistivity-Temperature Behavior of Intrinsically Conducting Bis(3-methoxysalicylideniminato)nickel Polymer.

Materials with a positive temperature coefficient have many applications, including overcharge and over-temperature protection in lithium-ion (Li-ion) batteries. The thermoresistive properties of an electrically conductive polymer, based on a Ni(salen)-type backbone, known as polyNiMeOSalen, were evaluated by means of in situ resistivity measurements. It was found that the polymer was conductive at temperatures below 220 °C; however, the polymer increased in resistivity by three orders of magnitude upon reaching 250 °C. Thermogravimetric results combined with elemental analyses revealed that the switch from the insulation stage to the conductive stage resulted from thermally dedoping the polymer. Electrochemical studies demonstrated that a polymer retains its electroactivity when it is heated and can be recovered to a conductive state through oxidation via electrochemical doping in an electrolyte solution.

Photocurrent in Multilayered Assemblies of Porphyrin-Fullerene Covalent Dyads: Evidence for Channels for Charge Transport.

Specially designed porphyrin-fullerene dyads have been synthesized to verify literature predictions based on quantum chemistry calculations that certain porphyrin-fullerene dyads are able to self-arrange into specific structures providing channels for charge transport in a bulk mass of organic compound. According to AFM and SEM data, the newly synthesized compounds were indeed prone to some kind of self-arrangement, although to a lesser degree than was expected. A dispersion corrected DFT study of the molecular non-covalent interactions performed at the DFT-D3 (B3LYP, 6-31G*) level of theory showed that the least energy corresponded to head-to-head dimers, with close contacts of porphyrin-porphyrin and fullerene-fullerene fragments, thus providing a unit building block of the channel for charge transport. Experimental proof for the existence of channels for charge transport was obtained by observing a photocurrent in a simple photovoltaic cell.