TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.

Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors: Kit, Kdr, Pdgfra. We used genome editing in mice to delete the TADs boundaries at the Kit locus and characterized chromatin folding and gene expression in pure cultures of fibroblasts, mast cells, and melanocytes. We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic activation only in melanocytes. Thus, the epigenetic landscape, namely the mutual arrangement of enhancers and actively transcribing genes, is important for predicting the consequences of the TAD boundaries removal. We also found that mice without a TAD border between the Kit and Kdr genes have a phenotypic manifestation of the mutation - a lighter coloration. Thus, the data obtained shed light on the principles of interaction between the 3D chromatin organization and epigenetic marks in the regulation of gene activity.

A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST.

NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.

Excess Enthalpies Analysis of Biofuel Components: Sunflower Oil-Alcohols Systems.

This study addresses the pressing issues of energy production and consumption, in line with global sustainable development goals. Focusing on the potential of alcohols as "green" alternatives to traditional fossil fuels, especially in biofuel applications, we investigate the thermochemical properties of three alcohols (n-propanol, n-butanol, n-pentanol) blended with sunflower oil. The calorimetric analysis allows for the experimental determination of excess enthalpies in pseudo-binary mixtures at 303.15 K, revealing similarities in the trends of the curves (dependence on concentrations) but with different values for the excess enthalpies for each mixture. Despite the structural differences of the alcohols studied, the molar excess enthalpy values exhibit uniformity, suggesting consistent mixing behavior. The peak values of excess enthalpies for systems with sunflower oil and n-propanol, n-butanol and n-pentanol are, respectively, 3255.2 J/mole, 3297.4 J/mole and 3150.1 J/mole. Both the NRTL and Redlich-Kister equations show satisfactory agreement with the obtained values.

Ultrastructural Abnormalities in Induced Pluripotent Stem Cell-Derived Neural Stem Cells and Neurons of Two Cohen Syndrome Patients.

Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.

Synthesis of chroman-annulated cyclopropanols via photoinduced intramolecular [2 + 1]-cycloaddition of 2-allyloxybenzaldehydes.

2-Allyloxybenzaldehydes undergo [2 + 1] cycloadditions under 365 nm LED irradiation to form the corresponding chroman-fused cyclopropanols. The reaction proceeds easily without any catalysts or additives in dimethyl sulfoxide.

Aerosol optical properties over the South Atlantic and southern ocean during the 2010-2012 summer seasons as part of the global maritime aerosol network.

Aerosols have implications to climate and biogeochemical cycles in the global oceans. At sites under indirect influence of dust emitted by the Patagonian semi-desert, a debate exists on the potential fertilization effects of iron enriched aerossol. Considering this subject we conducted measurements of aerosols optical properties using a Microtops II sun photometer to access aerosol size distributions and other intrinsic properties oversea from Atlantic Southern mid-latitudes to Antarctica. Oceanographic cruises were developed between December 2010 to April 2011 and October 2011 to April 2012, in the context of the Brazilian Antarctic Program, and between November 2011 to December 2011. This survey was taken as part of the Global Maritime Aerosol Network (MAN/NASA). Our data of AOD (500 nm) along the South American coast depicts a steady decrease southwards following the decreased latitudinal continental extent. However, the influence of the aerosols blown from Patagonia semi-desert region was clear from latitude 53°S to 64°S. The predominance of aerosol fine mode was observed in Central Atlantic and close to the Drake Passage. An unexpected aerosol coarse mode predominance was found close to the Antarctic Peninsula. We attribute that to a possible weathering of rock outcrops due to the strong westerly winds in that region.

A route to high-accuracy ab initio description of electronic excited states in high-spin lanthanide-containing species: A case study of GdO.

Accurate description of electronic excited states of high-spin molecular species is a yet unsolved problem in modern electronic structure theory. A composite computational scheme developed in the present work contributes to solving this task for a challenging case of lanthanide-containing molecules. In the scheme, the highest-spin states whose wavefunctions are dominated by a single Slater determinant are described at the single-reference (SR) CCSD(T) level, whereas the lower-spin states, being inherently multiconfigurational in their nature, are treated with multireference (MR) methods, MRCI and/or CASPT2. An original technique which scales MR results against SR CCSD(T) ones to improve the accuracy in the former is proposed and examined, taking the example of 12 electronic states of gadolinium monoxide, X9Σ-, Y7Σ-, A'9Δ, A1'7Δ, A9Π, A17Π, B9Σ-, B17Σ-, C9Π, C17Π, D9Σ-, and D17Σ-, up to 35 000 cm-1. A multitude of the corresponding Ω (spin-coupled) states was then studied within the state-interacting approach employing the full Breit-Pauli spin-orbit coupling operator with CASSCF-generated ΛS states as a basis. For all ΛS and Ω states, the Gd-O bond lengths, spectroscopic constants ωe, ωexe, αe, and adiabatic excitation energies are obtained. The theoretical predictions are in good agreement with the experimental data, with deviations in excitation energies not exceeding 350 cm-1 (1 kcal/mol). The spectroscopic properties of the yet unobserved electronic states, A'9Δ, A1'7Δ, C9Π, C17Π, D9Σ-, and D17Σ-, are evaluated for the first time.

Selective Area Epitaxy of Highly Strained InGaAs Quantum Wells (980-990 nm) in Ultrawide Windows Using Metalorganic Chemical Vapor Deposition.

We employed the selective-area-epitaxy technique using metalorganic chemical vapor deposition to fabricate and study samples of semiconductor heterostructures that incorporate highly strained InGaAs quantum wells (980-990 nm emission wavelength). Selective area epitaxy of InGaAs quantum wells was performed on templates that had a patterned periodic structure consisting of a window (where epitaxial growth occurred) and a passive mask (where epitaxial growth was suppressed), each with a width of 100 µm for every element. Additionally, a selectively grown potential barrier layer was included, which was characterized by an almost parabolic curvature profile of the surface. We conducted a study on the influence of the curvature profile of the growth surface on the optical properties of InGaAs quantum wells and the spatial distribution of composition in an ultrawide window. Our results showed that, under fixed selective-area-epitaxy conditions, the composition of the InxGa1-xAs and the wavelength of the quantum-well emission changed across the width of the window. Our study demonstrates that increasing the curvature profile of the growth surface of highly strained quantum wells leads to a transition in the photoluminescence wavelength distribution profile across the window, from quasi-parabolic to inverted parabolic.

An Optical-Fiber-Based Key for Remote Authentication of Users and Optical Fiber Lines.

We have shown the opportunity to use the unique inhomogeneities of the internal structure of an optical fiber waveguide for remote authentication of users or an optic fiber line. Optical time domain reflectometry (OTDR) is demonstrated to be applicable to observing unclonable backscattered signal patterns at distances of tens of kilometers. The physical nature of the detected patterns was explained, and their characteristic spatial periods were investigated. The patterns are due to the refractive index fluctuations of a standard telecommunication fiber. We have experimentally verified that the patterns are an example of a physically unclonable function (PUF). The uniqueness and reproducibility of the patterns have been demonstrated and an outline of authentication protocol has been proposed.

Meta-CF3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism.

In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.

NanoLuc Luciferase as a Fluorogen-Activating Protein for GFP Chromophore Based Fluorogens.

In this work, we showed that the well-known NanoLuc luciferase can act as a fluorogen activating protein for various arylidene-imidazolones structurally similar to the Kaede protein chromophore. We showed that such compounds can be used as fluorescent sensors for this protein and can also be used in pairs with it in fluorescent microscopy as a genetically encoded tag.

Crystal Structure, Raman, FTIR, UV-Vis Absorption, Photoluminescence Spectroscopy, TG-DSC and Dielectric Properties of New Semiorganic Crystals of 2-Methylbenzimidazolium Perchlorate.

Single crystals of 2-methylbenzimidazolium perchlorate were prepared for the first time with a slow evaporation method from an aqueous solution of a mixture of 2-methylbenzimidazole (MBI) crystals and perchloric acid HClO4. The crystal structure was determined by single crystal X-ray diffraction (XRD) and confirmed by XRD of powder. Angle-resolved polarized Raman and Fourier-transform infrared (FTIR) absorption spectra of crystals consist of lines caused by molecular vibrations in MBI molecule and ClO4- tetrahedron in the region ν = 200-3500 cm-1 and lattice vibrations in the region of 0-200 cm-1. Both XRD and Raman spectroscopy show a protonation of MBI molecule in the crystal. An analysis of ultraviolet-visible (UV-Vis) absorption spectra gives an estimation of an optical gap Eg~3.9 eV in the crystals studied. Photoluminescence spectra of MBI-perchlorate crystals consist of a number of overlapping bands with the main maximum at Ephoton ≅ 2.0 eV. Thermogravimetry-differential scanning calorimetry (TG-DSC) revealed the presence of two first-order phase transitions with different temperature hysteresis at temperatures above room temperature. The higher temperature transition corresponds to the melting temperature. Both phase transitions are accompanied by a strong increase in the permittivity and conductivity, especially during melting, which is similar to the effect of an ionic liquid.

Function and Evolution of the Loop Extrusion Machinery in Animals.

Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.

Indirect bandgap MoSe2 resonators for light-emitting nanophotonics.

Transition metal dichalcogenides (TMDs) are promising for new generation nanophotonics due to their unique optical properties. However, in contrast to direct bandgap TMD monolayers, bulk samples have an indirect bandgap that restricts their application as light emitters. On the other hand, the high refractive index of these materials allows for effective light trapping and the creation of high-Q resonators. In this work, a method for the nanofabrication of microcavities from indirect TMD multilayer flakes, which makes it possible to achieve pronounced resonant photoluminescence enhancement due to the cavity modes, is proposed. Whispering gallery mode (WGM) resonators are fabricated from bulk indirect MoSe2 using resistless scanning probe lithography. A micro-photoluminescence (µ-PL) investigation revealed the WGM spectra of the resonators with an enhancement factor up to 100. The characteristic features of WGMs are clearly seen from the scattering experiments which are in agreement with the results of numerical simulations. It is shown that the PL spectra in the fabricated microcavities are contributed by two mechanisms demonstrating different temperature dependences. The indirect PL, which is quenched with the temperature decrease, and the direct PL which almost does not depend on the temperature. The results of the work show that the suggested approach has great prospects in nanophotonics.

Multi-Frequency Light Sources Based on CVD Diamond Matrices with a Mix of SiV- and GeV- Color Centers and Tungsten Complexes.

Recently, nanodiamonds with negatively charged luminescent color centers based on atoms of the fourth group (SiV-, GeV-) have been proposed for use as biocompatible luminescent markers. Further improvement of the functionality of such systems by expanding the frequencies of the emission can be achieved by the additional formation of luminescent tungsten complexes in the diamond matrix. This paper reports the creation of diamond matrices by a hot filament chemical vapor deposition method, containing combinations of luminescing Si-V and Ge-V color centers and tungsten complexes. The possibility is demonstrated of creating a multicolor light source combining the luminescence of all embedded emitters. The emission properties of tungsten complexes and Si-V and Ge-V color centers in the diamond matrices were investigated, as well as differences in their luminescent properties and electron-phonon interaction at different temperatures.

[1,5]-Hydride Shift Triggered N-Dealkylative Cyclization into 2-Oxo-1,2,3,4-tetrahydroquinoline-3-carboxylates via Boronate Complexes.

A new simple one-pot two-step protocol for the synthesis of 2-oxo-1,2,3,4-tetrahydroquinoline-3-carboxylate from 2-(2-(benzylamino)benzylidene)malonate under the action of BF3·Et2O was developed. It was shown that the reaction proceeds through the formation of a stable iminium intermediate containing a difluoroboryl bridge in the dicarbonyl fragment of the molecule.

The human EF1a promoter does not provide expression of the transgene in mice.

In this work, we set out to create mice susceptible to the SARS-CoV-2 coronavirus. To ensure the ubiquitous expression of the human ACE2 gene we used the human EF1a promoter. Using pronuclear microinjection of the transgene construct, we obtained six founders with the insertion of the EF1a-hACE2 transgene, from which four independent mouse lines were established. Unfortunately, only one line had low levels of hACE2 expression in some organs. In addition, we did not detect the hACE2 protein in primary lung fibroblasts from any of the transgenic lines. Bisulfite sequencing analysis revealed that the EF1a promoter was hypermethylated in the genomes of transgenic animals. Extensive analysis of published works about transgenic animals indicated that EF1a transgenic constructs are frequently inactive. Thus, our case cautions against using the EF1a promoter to generate transgenic animals, as it is prone to epigenetic silencing.

Quark and Gluon Form Factors in Four-Loop QCD.

We compute the photon-quark and Higgs-gluon form factors to four-loop order within massless perturbative quantum chromodynamics. Our results constitute ready-to-use building blocks for N^{4}LO cross sections for Drell-Yan processes and gluon-fusion Higgs boson production at the LHC. We present complete analytic expressions for both form factors and show several of the most complicated master integrals.

Electron Spin Resonance of the Interacting Spinon Liquid.

We report experimental verification of the recently predicted collective modes of spinons, stabilized by backscattering interaction, in a model quantum spin chain material. We exploit the unique geometry of uniform Dzyaloshinskii-Moriya interactions in K_{2}CuSO_{4}Br_{2} to measure the interaction-induced splitting between the two components of the electron spin resonance (ESR) response doublet. From that we directly determine the magnitude of the "marginally irrelevant" backscattering interaction between spinons for the first time.