Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.

Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop new strategies to enable advanced data querying. Many databases have been developed to provide information about enhancers, but a schema that allows the standardized representation of data, securing interoperability between resources, has been lacking. In this work, we use knowledge graphs for the standardized representation of enhancers and topologically associating domains, together with data about their target genes, transcription factors, location on the human genome, and functional data about diseases and gene ontology annotations. We used this schema to integrate twenty-five enhancer datasets and two domain datasets, creating the most powerful integrative resource in this field to date. The knowledge graphs have been implemented using the Resource Description Framework and integrated within the open-access BioGateway knowledge network, generating a resource that contains an interoperable set of knowledge graphs (enhancers, TADs, genes, proteins, diseases, GO terms, and interactions between domains). We show how advanced queries, which combine functional and location restrictions, can be used to develop new hypotheses about functional aspects of gene expression regulation.

From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited.

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Divergent synthesis of benzoxaphospholenes and phosphacoumarins via the reaction of 2-alkenylphenols with phosphorus(III/V) chlorides.

The divergent synthesis of benzo[e]-1,2-oxaphosphinines or benzo[d]-1,2-oxaphospholenes along with spirocyclic quasiphosphonium compounds based on 2-alkenylphenols and phosphorus(III/V) chlorides is presented. The reaction is condition-dependent and determined by the biphility of the phosphorus(III) derivative and the dual reactivity of 2-alkenylphenol. The procedures are applicable for obtaining benzo[e]-1,2-oxaphosphinines substituted at position 4 and disubstituted at positions 4 and 5 as well as 3,3-disubstituted benzo[d]-1,2-oxaphospholenes with good to high yields.

Unraveling the effect of aromaticity for the dynamics of excited states of single benzene fluorophores.

The photophysical properties of a series of recently synthesized single benzene fluorophores were investigated using ensemble density functional theory calculations. The energetic stability of the ground and excited state species were counterposed against the aromaticity index derived from local vibrational modes. It was found that the large Stokes shift of the fluorophores (up to ca. 5800 cm - 1 ) originates from the effect of electron donating and electron withdrawing substituents rather than π -delocalization and related (anti-)aromaticity. On the basis of nonadiabatic molecular dynamics simulations, the absence of fluorescence from one of the regioisomers was explained by the occurrence of easily accessible S 1 /S 0 conical intersections below the vertical excitation energy level. It is demonstrated in the manuscript that the analysis of local mode force constants and the related aromaticity index represent a useful tool for the characterization of π -delocalization effects in π -conjugated compounds.

Bioprinting Using Organ Building Blocks: Spheroids, Organoids, and Assembloids.

Three-dimensional (3D) bioprinting, a promising advancement in tissue engineering technology, involves the robotic, layer-by-layer additive biofabrication of functional 3D tissue and organ constructs. This process utilizes biomaterials, typically hydrogels and living cells, following digital models. Traditional tissue engineering uses a classic triad of living cells, scaffolds, and physicochemical signals in bioreactors. A scaffold is a temporary, often biodegradable, support structure. Tissue engineering primarily falls into two categories: (i) scaffold based and (ii) scaffold free. The latter, scaffold-free 3D bioprinting, is gaining increasing popularity. Organ building blocks (OBB), capable of self-assembly and self-organization, such as tissue spheroids, organoids, and assembloids, have begun to be utilized in scaffold-free bioprinting. This article discusses the expanding range of OBB, presents the rapidly evolving collection of bioprinting and bioassembly methods using these OBB, and finally, outlines the advantages, challenges, and future perspectives of using OBB in organ printing.

Biomimetic crimped/aligned microstructure to optimize the mechanics of fibrous hybrid materials for compliant vascular grafts.

The precise mechanical properties of many tissues are highly dependent on both the composition and arrangement of the nanofibrous extracellular matrix. It is well established that collagen nanofibers exhibit a crimped microstructure in several tissues such as blood vessel, tendon, and heart valve. This collagen fiber arrangement results in the classic non-linear 'J-shaped' stress strain curve characteristic of these tissues. Synthetic biomimetic fibrous materials with a crimped microstructure similar to natural collagen demonstrate similar mechanical properties to natural tissues. The following work describes a nanofabrication method based on electrospinning used to fabricate two component hybrid electrospun fibrous materials that mimic the microstructure and mechanical properties of vascular tissue. The properties of these samples can be precisely and predictably optimized by modifying fabrication parameters. Tubular grafts with biomimetic microstructure were constructed to demonstrate the potential of this fabrication method in vascular graft replacement applications. It was possible to closely match both the overall geometry and the compliance of specific blood vessels by optimizing graft microstructure.

Novel Mitochondria-Targeted Amphiphilic Aminophosphonium Salts and Lipids Nanoparticles: Synthesis, Antitumor Activity and Toxicity.

The creation of mitochondria-targeted vector systems is a new tool for the treatment of socially significant diseases. Phosphonium groups provide targeted delivery of drugs through biological barriers to organelles. For this purpose, a new class of alkyl(diethylAmino)(Phenyl) Phosphonium halides (APPs) containing one, two, or three diethylamino groups was obtained by the reaction of alkyl iodides (bromides) with (diethylamino)(phenyl)phosphines under mild conditions (20 °C) and high yields (93-98%). The structure of APP was established by NMR and XRD. A high in vitro cytotoxicity of APPs against M-HeLa, HuTu 80, PC3, DU-145, PANC-1, and MCF-7 lines was found. The selectivity index is in the range of 0.06-4.0 µM (SI 17-277) for the most active APPs. The effect of APPs on cancer cells is characterized by hyperproduction of ROS and depolarization of the mitochondrial membrane. APPs induce apoptosis, proceeding along the mitochondrial pathway. Incorporation of APPs into lipid systems (liposomes and solid lipid nanoparticles) improves cytotoxicity toward tumor cells and decrease toxicity against normal cell lines. The IC50s of lipid systems are lower than for the reference drug DOX, with a high SI (30-56) toward MCF-7 and DU-145. APPs exhibit high selective activity against Gram-positive bacteria S. aureus 209P and B. segeus 8035, including methicillin-resistant S. aureus (MRSA-1, MRSA-2), comparable to the activity of the fluoroquinolone antibiotic norfloxacin. A moderate in vivo toxicity in CD-1 mice was established for the lead APP.

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures.

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.

Degradation of Structurally Modified Polylactide under the Controlled Composting of Food Waste.

The degradation of polylactide (PLA) films of different structures under conditions of controlled composting has been studied. We have demonstrated that PLA underwent degradation within one month in a substrate that simulated standard industrial composting. Regardless of the initial structure of the samples, the number-average molecular weight (Mn) decreased to 4 kDa while the degree of crystallinity increased to about 70% after 21 days of composting. Addition of an inoculant to the standard substrate resulted in the accelerated degradation of the PLA samples for one week due to an abiotic hydrolysis. These findings have confirmed that industrial composting could solve the problem of plastic disposal at least for PLA.

Bifunctionalized Betulinic Acid Conjugates with C-3-Monodesmoside and C-28-Triphenylphosphonium Moieties with Increased Cancer Cell Targetability.

A convenient synthesis is presented for a new class of bioactive bifunctionalized conjugates of lupane-type triterpenoids with triphenylphosphonium (TPP) and glycopyranosyl targeting moieties. The main synthesis steps include glycosylation of haloalkyl esters of the triterpene acid at the C-3 position by the imidate derivatives of glycopyranose followed by the product modification at the C-28 position with triphenylphosphine. The conjugates of betulinic acid (BetA) with TPP and d-glucose, l-rhamnose, or d-mannose moieties were thus synthesized as potential next-generation BetA-derived anticancer compounds. LC-MS/MS analysis in glucose-free physiological solution indicated that the glycosides showed better accumulation in PC-3 prostate cancer cells than both BetA and TPP-BetA conjugate, while the transporting effect of monosaccharide residues increased as follows: d-mannose < l-rhamnose ≈ d-glucose. At saturated concentrations, the glycosides caused a disturbing effect on mitochondria with a more drastic drop in transmembrane potential but weaker overproduction of mitochondrial reactive oxygen species (ROS) compared to TPP-BetA conjugate. Cytotoxicity of the glycosides in culture medium was comparable with or higher than that of the nonglycosylated conjugate, depending on the cancer cell line, whereas the compounds were less active toward primary fibroblasts. Glycosylation tended to increase pro-apoptotic and decrease pro-autophagic activities of the BetA derivatives. Cytotoxicity of the synthesized glycosides was considered in comparison with the summarized data on the natural and modified BetA glycosides. The results obtained are important for the development of bifunctionalized conjugates of triterpenoids with an increased cancer cell targetability.

High-performance strategies for the recent MRSF-TDDFT in GAMESS.

Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios.

Commercial articulated collaborative in situ 3D bioprinter for skin wound healing.

In situ bioprinting is one of the most clinically relevant techniques in the emerging bioprinting technology because it could be performed directly on the human body in the operating room and it does not require bioreactors for post-printing tissue maturation. However, commercial in situ bioprinters are still not available on the market. In this study, we demonstrated the benefit of the originally developed first commercial articulated collaborative in situ bioprinter for the treatment of full-thickness wounds in rat and porcine models. We used an articulated and collaborative robotic arm from company KUKA and developed original printhead and correspondence software enabling in situ bioprinting on curve and moving surfaces. The results of in vitro and in vivo experiments show that in situ bioprinting of bioink induces a strong hydrogel adhesion and enables printing on curved surfaces of wet tissues with a high level of fidelity. The in situ bioprinter was convenient to use in the operating room. Additional in vitro experiments (in vitro collagen contraction assay and in vitro 3D angiogenesis assay) and histological analyses demonstrated that in situ bioprinting improves the quality of wound healing in rat and porcine skin wounds. The absence of interference with the normal process of wound healing and even certain improvement in the dynamics of this process strongly suggests that in situ bioprinting could be used as a novel therapeutic modality in wound healing.

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells.

Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.

Novel triphenylphosphonium amphiphilic conjugates of glycerolipid type: synthesis, cytotoxic and antibacterial activity, and targeted cancer cell delivery.

This work deals with the creation of new cationic triphenylphosphonium amphiphilic conjugates of glycerolipid type (TPP-conjugates), bearing a pharmacophore terpenoid fragment (abietic acid and betulin) and a fatty acid residue in one hybrid molecule as a new generation of antitumor agents with high activity and selectivity. The TPP-conjugates showed high mitochondriotropy leading to the development of mitochondriotropic delivery systems such as TPP-pharmacosomes and TPP-solid lipid particles. Introducing the betulin fragment into the structure of a TPP-conjugate (compound 10) increases the cytotoxicity 3 times towards tumor cells of prostate adenocarcinoma DU-145 and 4 times towards breast carcinoma MCF-7 compared to TPP-conjugate 4a in the absence of betulin. TPP-hybrid conjugate 10 with two pharmacophore fragments, betulin and oleic acid, has significant cytotoxicity toward a wide range of tumor cells. The lowest IC50 of 10 is 0.3 µM toward HuTu-80. This is at the level of the reference drug doxorubicin. TPP-pharmacosomes (10/PC) increased the cytotoxic effect approximately 3 times toward HuTu-80 cells, providing high selectivity (SI = 480) compared to the normal liver cell line Chang liver.

Advantages and Potential Benefits of Using Organoids in Nanotoxicology.

Organoids are microtissues that recapitulate the complex structural organization and functions of tissues and organs. Nanoparticles have several specific properties that must be considered when replacing animal models with in vitro studies, such as the formation of a protein corona, accumulation, ability to overcome tissue barriers, and different severities of toxic effects in different cell types. An increase in the number of articles on toxicology research using organoid models is related to an increase in publications on organoids in general but is not related to toxicology-based publications. We demonstrate how the quantitative assessment of toxic changes in the structure of organoids and the state of their cell collections provide more valuable results for toxicological research and provide examples of research methods. The impact of the tested materials on organoids and their differences are also discussed. In conclusion, we highlight the main challenges, the solution of which will allow researchers to approach the replacement of in vivo research with in vitro research: biobanking and standardization of the structural characterization of organoids, and the development of effective screening imaging techniques for 3D organoid cell organization.

Phosphineoxide-Chelated Europium(III) Nanoparticles for Ceftriaxone Detection.

The present work demonstrates the optimization of the ligand structure in the series of bis(phosphine oxide) and ß-ketophosphine oxide representatives for efficient coordination of Tb3+ and Eu3+ ions with the formation of the complexes exhibiting high Tb3+- and Eu3+-centered luminescence. The analysis of the stoichiometry and structure of the lanthanide complexes obtained using the XRD method reveals the great impact of the bridging group nature between two phosphine oxide moieties on the coordination mode of the ligands with Tb3+ and Eu3+ ions. The bridging imido-group facilitates the deprotonation of the imido- bis(phosphine oxide) ligand followed by the formation of tris-complexes. The spectral and PXRD analysis of the separated colloids indicates that the high stability of the tris-complexes provides their safe conversion into polystyrenesulfonate-stabilized colloids using the solvent exchange method. The red Eu3+-centered luminescence of the tris-complex exhibits the same specificity in the solutions and the colloids. The pronounced luminescent response on the antibiotic ceftriaxone allows for sensing the latter in aqueous solutions with an LOD value equal to 0.974 µM.

Interplay of Anisotropic Exchange Interactions and Single-Ion Anisotropy in Single-Chain Magnets Built from Ru/Os Cyanidometallates(III) and Mn(III) Complex.

Two novel 1D heterobimetallic compounds {[MnIII(SB2+)MIII(CN)6]·4H2O}n (SB2+ = N,N'-ethylenebis(5-trimethylammoniomethylsalicylideneiminate) based on orbitally degenerate cyanidometallates [OsIII(CN)6]3- (1) and [RuIII(CN)6]3- (2) and MnIII Schiff base complex were synthesized and characterized structurally and magnetically. Their crystal structures consist of electrically neutral, well-isolated chains composed of alternating [MIII(CN)6]3- anions and square planar [MnIII(SB2+)]3+ cations bridged by cyanide groups. These -ion magnetic anisotropy of MnIII centers. These results indicate that the presence of compounds exhibit single-chain magnet (SCM) behavior with the energy barriers of Δτ1/kB = 73 K, Δτ2/kB = 41.5 K (1) and Δτ1/kB = 51 K, Δτ2 = 27 K (2). Blocking temperatures of TB = 2.8, 2.1 K and magnetic hysteresis with coercive fields (at 1.8 K) of 8000, 1600 Oe were found for 1 and 2, respectively. Theoretical analysis of the magnetic data reveals that their single-chain magnet behavior is a product of a complicated interplay of extremely anisotropic triaxial exchange interactions in MIII(4d/5d)-CN-MnIII fragments: -JxSMxSMnx-JySMySMny-JzSMzSMnz, with opposite sign of exchange parameters Jx = -22, Jy = +28, Jz = -26 cm-1 and Jx = -18, Jy = +20, Jz = -18 cm-1 in 1 and 2, respectively) and single orbitally degenerate [OsIII(CN)6]3- and [RuIII(CN)6]3- spin units with unquenched orbital angular momentum in the chain compounds 1 and 2 leads to a peculiar regime of slow magnetic relaxation, which is beyond the scope of the conventional Glaubers's 1D Ising model and anisotropic Heisenberg model.

Fluorescence Imaging of Cell Membrane Potential: From Relative Changes to Absolute Values.

Membrane potential is a fundamental property of biological cells. Changes in membrane potential characterize a vast number of vital biological processes, such as the activity of neurons and cardiomyocytes, tumorogenesis, cell-cycle progression, etc. A common strategy to record membrane potential changes that occur in the process of interest is to utilize organic dyes or genetically-encoded voltage indicators with voltage-dependent fluorescence. Sensors are introduced into target cells, and alterations of fluorescence intensity are recorded with optical methods. Techniques that allow recording relative changes of membrane potential and do not take into account fluorescence alterations due to factors other than membrane voltage are already widely used in modern biological and biomedical studies. Such techniques have been reviewed previously in many works. However, in order to investigate a number of processes, especially long-term processes, the measured signal must be corrected to exclude the contribution from voltage-independent factors or even absolute values of cell membrane potential have to be evaluated. Techniques that enable such measurements are the subject of this review.

Prototropically Controlled Dynamics of Cytosine Photodecay.

The effect of the existence of several prototropic tautomers of cytosine on its UV/vis spectra and the excited state decay dynamics is studied by spectral and nonadiabatic molecular dynamics (NAMD) simulations in connection with the mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Simulated UV/vis spectra provide a strong indication that the H3N keto-amino cytosine tautomer (the least anticipated species) may be present under experimental conditions. The NAMD simulations yield a wide range of excited state decay constants for various tautomers of cytosine, ranging from ∼1.3 ps for the biologically relevant H1N keto-amino tautomer to ∼0.1 ps for the keto-imino tautomer. The slowness of the H1N decay dynamics follows from the presence of a barrier on the excited state energy surface separating the Franck-Condon structure from the major decay funnel, the conical intersection seam. It is suggested that the experimentally observed photodecay dynamics may result from a combination of the decay processes of various tautomers (H3N in particular) present simultaneously under the experimental conditions.

Terpenes-Modified Lipid Nanosystems for Temozolomide, Improving Cytotoxicity against Glioblastoma Human Cancer Cells In Vitro.

Currently, increasing the efficiency of glioblastoma treatment is still an unsolved problem. In this study, a combination of promising approaches was proposed: (i) an application of nanotechnology approach to create a new terpene-modified lipid system (7% w/w), using soybean L-α-phosphatidylcholine, N-carbonyl-methoxypolyethylene glycol-2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine for delivery of the chemotherapy drug, temozolomide (TMZ, 1 mg/mL); (ii) use of TMZ associated with natural compounds-terpenes (1% w/w) abietic acid and Abies sibirica Ledeb. resin (A. sibirica). Different concentrations and combinations of terpene-lipid systems were employed to treat human cancer cell lines T 98G (glioblastoma), M-Hela (carcinoma of the cervix) and human liver cell lines (Chang liver). The terpene-lipid systems appeared to be unilamellar and of spherical shape under transmission electron microscopy (TEM). The creation of a TMZ-loaded terpene-lipid nanosystem was about 100 nm in diameter with a negative surface charge found by dynamic light scattering. The 74% encapsulation efficiency allowed the release time of TMZ to be prolonged. The modification by terpenes of TMZ-loaded lipid nanoparticles improved by four times the cytotoxicity against human cancer T 98G cells and decreased the cytotoxicity against human normal liver cells. Terpene-modified delivery lipid systems are of potential interest as a combination therapy.