Structure-guided reprogramming of human cGAS dinucleotide linkage specificity.

Cyclic dinucleotides (CDNs) play central roles in bacterial pathogenesis and innate immunity. The mammalian enzyme cGAS synthesizes a unique cyclic dinucleotide (cGAMP) containing a 2'-5' phosphodiester linkage essential for optimal immune stimulation, but the molecular basis for linkage specificity is unknown. Here, we show that the Vibrio cholerae pathogenicity factor DncV is a prokaryotic cGAS-like enzyme whose activity provides a mechanistic rationale for the unique ability of cGAS to produce 2'-5' cGAMP. Three high-resolution crystal structures show that DncV and human cGAS generate CDNs in sequential reactions that proceed in opposing directions. We explain 2' and 3' linkage specificity and test this model by reprogramming the human cGAS active site to produce 3'-5' cGAMP, leading to selective stimulation of alternative STING adaptor alleles in cells. These results demonstrate mechanistic homology between bacterial signaling and mammalian innate immunity and explain how active site configuration controls linkage chemistry for pathway-specific signaling.

Frequent winners explain apparent skewness preferences in experience-based decisions.

Do people's attitudes toward the (a)symmetry of an outcome distribution affect their choices? Financial investors seek return distributions with frequent small returns but few large ones, consistent with leading models of choice in economics and finance that assume right-skewed preferences. In contrast, many experiments in which decision-makers learn about choice options through experience find the opposite choice tendency, in favor of left-skewed options. To reconcile these seemingly contradicting findings, the present work investigates the effect of skewness on choices in experience-based decisions. Across seven studies, we show that apparent preferences for left-skewed outcome distributions are a consequence of those distributions having a higher value in most direct outcome comparisons, a "frequent-winner effect." By manipulating which option is the frequent winner, we show that choice tendencies for frequent winners can be obtained even with identical outcome distributions. Moreover, systematic choice tendencies in favor of right- or left-skewed options can be obtained by manipulating which option is experienced as the frequent winner. We also find evidence for an intrinsic preference for right-skewed outcome distributions. The frequent-winner phenomenon is robust to variations in outcome distributions and experimental paradigms. These findings are confirmed by computational analyses in which a reinforcement-learning model capturing frequent winning and intrinsic skewness preferences provides the best account of the data. Our work reconciles conflicting findings of aggregated behavior in financial markets and experiments and highlights the need for theories of decision-making sensitive to joint outcome distributions of the available options.

Nontriplet feature of genetic code in Euplotes ciliates is a result of neutral evolution.

The triplet nature of the genetic code is considered a universal feature of known organisms. However, frequent stop codons at internal mRNA positions in Euplotes ciliates ultimately specify ribosomal frameshifting by one or two nucleotides depending on the context, thus posing a nontriplet feature of the genetic code of these organisms. Here, we sequenced transcriptomes of eight Euplotes species and assessed evolutionary patterns arising at frameshift sites. We show that frameshift sites are currently accumulating more rapidly by genetic drift than they are removed by weak selection. The time needed to reach the mutational equilibrium is several times longer than the age of Euplotes and is expected to occur after a several-fold increase in the frequency of frameshift sites. This suggests that Euplotes are at an early stage of the spread of frameshifting in expression of their genome. In addition, we find the net fitness burden of frameshift sites to be noncritical for the survival of Euplotes. Our results suggest that fundamental genome-wide changes such as a violation of the triplet character of genetic code can be introduced and maintained solely by neutral evolution.

HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases.

The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.

Identification of essential sites of lipid peroxidation in ferroptosis.

Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, provides a potential treatment avenue for drug-resistant cancers and may play a role in the pathology of some degenerative diseases. Identifying the subcellular membranes essential for ferroptosis and the sequence of their peroxidation will illuminate drug discovery strategies and ferroptosis-relevant disease mechanisms. In this study, we employed fluorescence and stimulated Raman scattering imaging to examine the structure-activity-distribution relationship of ferroptosis-modulating compounds. We found that, although lipid peroxidation in various subcellular membranes can induce ferroptosis, the endoplasmic reticulum (ER) membrane is a key site of lipid peroxidation. Our results suggest an ordered progression model of membrane peroxidation during ferroptosis that accumulates initially in the ER membrane and later in the plasma membrane. Thus, the design of ER-targeted inhibitors and inducers of ferroptosis may be used to optimally control the dynamics of lipid peroxidation in cells undergoing ferroptosis.

The diamond-silicon carbide composite Skeleton® as a promising material for substrates of intense X-ray beam optics.

The paper considers the possibility of using the diamond-silicon carbide composite Skeleton® with a technological coating of polycrystalline silicon as a substrate for X-ray mirrors used with powerful synchrotron radiation sources (third+ and fourth generation). Samples were studied after polishing to provide the following surface parameters: root-mean-square flatness ≃ 50 nm, micro-roughness on the frame 2 µm × 2 µm σ ≃ 0.15 nm. The heat capacity, thermal conductivity and coefficient of linear thermal expansion were investigated. For comparison, a monocrystalline silicon sample was studied under the same conditions using the same methods. The value of the coefficient of linear thermal expansion turned out to be higher than that of monocrystalline silicon and amounted to 4.3 × 10-6 K-1, and the values of thermal conductivity (5.0 W cm-1 K-1) and heat capacity (1.2 J K-1 g-1) also exceeded the values for Si. Thermally induced deformations of both Skeleton® and monocrystalline silicon samples under irradiation with a CO2 laser beam have also been experimentally studied. Taking into account the obtained thermophysical constants, the calculation of thermally induced deformation under irradiation with hard (20 keV) X-rays showed almost three times less deformation of the Skeleton® sample than of the monocrystalline silicon sample.

Complete photonic bandgap in a low-index two-dimensional quasicrystalline structure.

A bandgap in the continuum spectrum of photons in addition to its basic physical significance has strong potential for applications. Analogous to semiconductor crystals for electrons, periodic dielectric structures named photonic crystals were proposed to control photon flux propagation. In our search for low refractive index (RI) structures with a photonic bandgap, initial research efforts were focused on photonic crystal design, while aperiodic structures allow lower values of refractive index contrast to sustain a photonic bandgap. Here, we report on a two-dimensional quasicrystalline structure designed as a set of one-dimensional lattices merged into a single binary structure made of two materials with refractive index contrast 2|n1 - n2|/(n1 + n2) = 0.16 and even less in theory. We confirmed the theoretical prediction of bandgap exciting by measuring the radiation suppression of a dipole source placed in the center of the quasicrystalline structure. The full-wave numerical simulations and the experimental study appear to be in good agreement with the theoretical model.

Characterization of a patient-derived variant of GPX4 for precision therapy.

Glutathione peroxidase 4 (GPX4), as the only enzyme in mammals capable of reducing esterified phospholipid hydroperoxides within a cellular context, protects cells from ferroptosis. We identified a homozygous point mutation in the GPX4 gene, resulting in an R152H coding mutation, in three patients with Sedaghatian-type spondylometaphyseal dysplasia. Using structure-based analyses and cell models, including patient fibroblasts, of this variant, we found that the missense variant destabilized a critical loop, which disrupted the active site and caused a substantial loss of enzymatic function. We also found that the R152H variant of GPX4 is less susceptible to degradation, revealing the degradation mechanism of the GPX4 protein. Proof-of-concept therapeutic treatments, which overcome the impaired R152H GPX4 activity, including selenium supplementation, selective antioxidants and a deuterated polyunsaturated fatty acid were identified. In addition to revealing a general approach to investigating rare genetic diseases, we demonstrate the biochemical foundations of therapeutic strategies targeting GPX4.

A matter of new life and cell death: programmed cell death in the mammalian ovary.

BACKGROUND: The mammalian ovary is a unique organ that displays a distinctive feature of cyclic changes throughout the entire reproductive period. The estrous/menstrual cycles are associated with drastic functional and morphological rearrangements of ovarian tissue, including follicular development and degeneration, and the formation and subsequent atrophy of the corpus luteum. The flawless execution of these reiterative processes is impossible without the involvement of programmed cell death (PCD). MAIN TEXT: PCD is crucial for efficient and careful clearance of excessive, depleted, or obsolete ovarian structures for ovarian cycling. Moreover, PCD facilitates selection of high-quality oocytes and formation of the ovarian reserve during embryonic and juvenile development. Disruption of PCD regulation can heavily impact the ovarian functions and is associated with various pathologies, from a moderate decrease in fertility to severe hormonal disturbance, complete loss of reproductive function, and tumorigenesis. This comprehensive review aims to provide updated information on the role of PCD in various processes occurring in normal and pathologic ovaries. Three major events of PCD in the ovary-progenitor germ cell depletion, follicular atresia, and corpus luteum degradation-are described, alongside the detailed information on molecular regulation of these processes, highlighting the contribution of apoptosis, autophagy, necroptosis, and ferroptosis. Ultimately, the current knowledge of PCD aberrations associated with pathologies, such as polycystic ovarian syndrome, premature ovarian insufficiency, and tumors of ovarian origin, is outlined. CONCLUSION: PCD is an essential element in ovarian development, functions and pathologies. A thorough understanding of molecular mechanisms regulating PCD events is required for future advances in the diagnosis and management of various disorders of the ovary and the female reproductive system in general.

Cyclocondensation of 2-(α-Diazoacyl)-2H-azirines with Amidines in Diazo Synthesis of Functionalized Naphtho[1,2-d]imidazoles.

A diazo approach toward functionalized naphtho[1,2-d]imidazole derivatives has been developed. It involved a new reaction of arylamidines with 2-(α-diazoacyl)-2H-azirines giving 5-aryl-4-(α-diazoacyl)-1H-imidazoles under mild conditions in good yields. The mechanism of annulation of azirines with amidines is discussed based on DFT calculations. The reaction proceeds in an unusual manner by cleavage of the azirine C-C bond, allowing for the transfer of the aryl substituent from the arylamidine to the proper position of the key intermediate of naphtho[1,2-d]imidazole synthesis. Under thermolysis conditions, 5-aryl-4-(α-diazoacyl)-1H-imidazoles undergo Wolff rearrangement followed by the selective 6π-cyclization of transient ketene to form 3H-naphtho[1,2-d]imidazoles bearing various substituents in the positions 2,3,4,5,7,8,9. Additionally, variation of the substituents at position 5 of naphtho[1,2-d]imidazoles is possible through the formation of triflates and subsequent cross-coupling reactions. One more heterocyclic pharmacophoric skeleton, 3H-furo[3',2':3,4]naphtho[1,2-d]imidazole, was easily constructed from methyl 5-hydroxy-3H-naphtho[1,2-d]imidazole-4-carboxylates in a one-pot mode using O-alkylation with phenacyl bromides followed by base-induced intramolecular acyl substitution at room temperature with high yields.

Regioselective Synthesis of Highly Functionalized 2H-Pyrroles via Dearomative Chlorination of 1H-Pyrroles.

An efficient protocol was developed for the synthesis of highly functionalized 2H-pyrroles. This synthetic approach involves the in situ generation of highly reactive 2,5-dichloro-substituted 2H-pyrroles through dearomative chlorination of the corresponding 1H-pyrroles. The resulting reaction mixture is then treated with various amines, leading to the formation of 2,5-diaminated 2H-pyrroles. Subsequent nucleophilic substitution of fluorine with different N-, O-, and S-nucleophiles allows us to introduce additional functionality into a 2H-pyrrole core. The overall outcome of this reaction sequence is the triple nucleophilic modification of pyrroles. All steps of the sequence were found to be highly efficient, regioselective in the preparation of desired di- and trisubstituted derivatives in up to 96% overall yield. In addition, the computational study of this reaction sequence was carried out using density functional theory (DFT). The results of calculations are in perfect agreement with experimental observations.

Sequential Modification of Pyrrole Ring with up to Three Different Nucleophiles.

An umpolung strategy was used for the preparation of highly functionalized 3-pyrrolin-2-ones. This approach involves dearomative double chlorination of 1H-pyrroles to form highly reactive dichloro-substituted 2H-pyrroles. The resulting intermediate reacts selectively with wet alcohols to form the corresponding alkoxy-substituted 3-pyrrolin-2-ones via double nucleophilic substitution in up to 99% yield. The subsequent reaction with different N-, O-, and S-nucleophiles opens access to highly functionalized pyrrolinones bearing additional functionality. The overall outcome of the reported sequence is step-by-step nucleophilic modification of pyrroles with three different nucleophiles. All steps were found to be highly efficient and 100% regioselective. This transformation proceeds under mild conditions and does not require any catalyst to give final products in very high yields. The obtained experimental results are in perfect agreement with the data obtained by theoretical investigation of these reactions.

Stable 2-Azaallyl Salts as a Bridge between 2H-Azirines and Densely Functionalized 2H-Pyrroles.

An efficient protocol for the synthesis of stable 2-azaallyl anion salts by the reaction of alkyl 2-bromo-2H-azirine-2-carboxylates with trimethylsilyl cyanide/Bu4NF has been developed. The domino reaction proceeds in four steps via the cleavage of the azirine C-C bond to provide the tetrabutylammonium salts of stereochemically pure 2-azaallyl anions having U-configuration relative to the cyano groups. The anions with an ortho-substituted aryl group or styryl group exist as a mixture of two geometrical isomers across the N2-C3 bond. 2-Azaallyl anion salts have been shown to be convenient substrates for the one-pot synthesis of densely functionalized 2H-pyrroles by the alkylation-cyclization sequence.

Fruit and seed structure in the ANA-grade angiosperms: Ancestral traits and specializations.

PREMISE: The representatives of the ANA-grade angiosperms demonstrate a diverse pattern of morphological characters, but their apocarpous gynoecium (except in Nymphaeaceae), composed of at least partly ascidiate carpels, the four-nucleate and four-celled female gametophyte, and the diploid endosperm (except in Amborella) are inferred to be plesiomorphies. Since the structure of fruits in Austrobaileyales is under-investigated, this research aims to fill this gap in these data, describing the carpological characters of ANA-grade taxa, and potentially illuminating the ancestral fruit and seed types of angiosperms. METHODS: The pericarp and seed coat anatomy was studied with light microscopy. The character optimization was carried out using WinClada software. RESULTS: The fruits of Austrobaileya, Trimenia, Kadsura, and Schisandra are determined to be apocarpous berries of the Schisandra type, with a parenchymatous pericarp and mesotestal (Austrobaileya) or exomesotestal seeds (other genera). Most inferred scenarios of fruit evolution indicate that the apocarpous berry is either the most probable plesiomorphic fruit type of all angiosperms, or that of all angiosperms except Amborellaceae. This inference suggests the early origin of the berry in fruit evolution. The plesiomorphic seed type of angiosperms according to reconstructed scenarios of seed type evolution was either a seed lacking a sclerenchymatous layer or an exotestal seed. CONCLUSIONS: The current research indicates that an apocarpous berry, and not a follicle, is a probable plesiomorphic character of the ANA-grade taxa and of angiosperms as a whole.

Synthesis of Technetium Carboxylates: Wheel-Like Octanuclear Clusters (Tc8(µ-O)8(RCOO)16, Where R = CF3, C6H5)─Potential Nanobuilding Units for Tc-MOFs.

Herein, we studied the behavior of TcO4- in trifluoroacetic anhydride (TFAA) under visible light irradiation in situ by UV-vis spectroscopy. One carboxylate of Tc(VII) C2F3O5Tc (1) and two wheel-like carboxylate clusters of Tc(IV) Tc8(µ-O)8(CF3COO)16 (2, 3) and Tc8(µ-O)8(C6H5COO)16 (4) were synthesized and analyzed using pXRD, TGA, UV-vis spectroscopy, and SCXRD techniques. According to SCXRD, it was found that Tc(IV) trifluoroacetate exists in two crystalline modifications. By UV-vis spectroscopy and DFT calculations, it was shown that the primary compound in the reaction system is trifluoroacetate Tc(VII). A technetium trifluoroacetate(VII) and Tc intermediates of unidentified nature both show photosensitivity. The influence of intermolecular noncovalent interactions on the volatility of trifluoroacetate and benzoate Tc(IV) is shown. The main regularities of chemical transformations of technetium in nonaqueous solutions of carboxylates have been revealed. The obtained data on the kinetics of the process suggest that technetium in trifluoroacetic anhydride can simultaneously exist in the form of Tc(VII), Tc(VI), Tc(V), and Tc(IV). Under laser ionization or prolonged heating, the formation of the Tc(II,III)-cluster is observed.

Application of the intramolecular Diels-Alder vinylarene (IMDAV) reaction for the synthesis of benzo-, carbocyclo-, thienothiopheneisoindolecarboxylic acids and its limitations.

Thienylallylamines, readily accessible from the corresponding thienyl aldehydes, react with maleic and trifluoromethylmaleic anhydrides leading to the formation of acids with a thieno[2,3-f]isoindole core. The reaction sequence involves two successive steps: acylation of the nitrogen atom of the initial allylamine and the intramolecular Diels-Alder vinylarene (IMDAV) reaction. The scope and limitations of the proposed method were thoroughly investigated. It has been revealed with the aid of X-ray analysis and DFT calculations that the key step, the IMDAV reaction, proceeds through an exo-transition state, giving rise to the exclusive formation of a single diastereomer of the target heterocycle. The obtained functionally substituted thieno[2,3-f]isoindole carboxylic acids are potentially useful substrates for further transformations and bioscreening. The antimicrobial evaluation of the obtained compounds revealed that 1-oxo-2-(3-(trifluoromethyl)phenyl)hexahydrobenzo[4,5]thieno[2,3-f]isoindole-10-carboxylic acid is the most active sample in the synthesized library. It exhibits antibacterial activity against sensitive strains of Gram-positive bacteria, including S. aureus, Enterococcus faecium, Bacillus cereus, and Micrococcus luteus, as well as the Gram-negative bacteria E. coli and Pseudomonas fluorescens, with MIC values ranging from 4 to 64 µg mL-1. 9-Oxo-8-phenyloctahydronaphtho[2,1-d]thieno[2,3-f]isoindole-10-carboxylic acid showed antifungal activity against yeast culture C. albicans with a MIC value of 32 µM.

Development of a reliable surgical quality assurance tool for gastrectomy in oncological trials.

BACKGROUND: Despite its recognized importance, there is currently no reliable tool for surgical quality assurance (SQA) of gastrectomy in surgical oncology. The aim of this study was to develop an SQA tool for gastrectomy and to apply this tool within the ADDICT Trial in order to assess the extent and completeness of lymphadenectomy. METHODS: The operative steps for D1+ and D2 gastrectomy have been previously described in the literature and ADDICT trial manual. Two researchers also performed fieldwork in the UK and Japan to document key operative steps through photographs and semi-structured interviews with expert surgeons. This provided the steps that were used as the framework for the SQA tool. Sixty-two photographic cases from the ADDICT Trial were rated by three independent surgeons. Generalizability (G) theory determined inter-rater reliability. D-studies examined the effect of varying the number of assessors and photographic series they rated. Chi-square assessed intra-rater reliability, comparing how the individual assessor's responses corresponded to their global rating for extent of lymphadenectomy. RESULTS: The tool comprised 20 items, including 19 anatomical landmarks and a global rating score. Overall reliability had G-coefficient of 0.557. Internal consistency was measured with a Cronbach's alpha score of 0.869 and Chi-square confirmed intra-rater reliability for each assessor as < 0.05. CONCLUSIONS: A photographic surgical quality assurance tool is presented for gastrectomy. Using this tool, the assessor can reliably determine not only the quality but also the extent of the lymphadenectomy performed based on remaining anatomy rather than the excised specimen.

Elongation of N6-benzyladenosine scaffold via Pd-catalyzed C-C bond formation leads to derivatives with antiflaviviral activity.

Decoration of nucleoside analogues with lipophilic groups often leads to compounds with improved antiviral activity. For example, N6-benzyladenosine derivatives containing elongated lipophilic substituents in the benzyl core efficiently inhibit reproduction of tick-borne encephalitis virus (TBEV), while N6-benzyladenosine itself potently inhibits reproduction of human enterovirus A71 (EV-A71). We have extended a series of N6-benzyladenosine analogues using effective synthetic methods of CC bond formation based on Pd-catalyzed cross-coupling reactions (Sonogashira and Suzuki) in order to study the influence of bulky lipophilic substituents in the N6 position of adenosine on the antiviral activity against flaviviruses, such as TBEV, yellow fever virus (YFV) and West Nile virus (WNV), as well as a panel of enteroviruses including EV-A71, Echovirus 30 (E30), and poliovirus type 2 (PV2). Reproduction of tested flaviviruses appeared to be inhibited by the micromolar concentrations of the compounds, while cytotoxicity in most cases was beyond the detection limit. Time-of-addition studies demonstrated that the hit compounds inhibited the stage of viral RNA synthesis, but not the stages of the viral entry or protein translation. As a result, several new promising antiflaviviral leads have been identified. On the other hand, none of the synthesized compounds inhibited enterovirus reproduction, indicating a possibility of involvement of flavivirus-specific pathways in their mechanism of action.

Conditions for the efficiency of optical limiting based on experiment and quantum chemical calculations.

The development of suitable protection against laser radiation has proven challenging due to the lack of predictive models. The purpose of this article is to exclude the existing drawback by creating a universal strategy based on correlations between experimental and theoretical data characterizing the nonlinear optical properties of absorbers, for which a series of low-symmetry penta(chloro)cyclotriphosphazene-substituted monophthalocyanines was chosen. To search for correlations on a small series of dyes, we used the advanced algorithm CORRELATO, which has been proven to construct even the most unusual relationships demonstrated in our previous works. Due to the reducing symmetry of molecules, large values of the nonlinear absorption coefficient (more than 3000 cm GW-1) and, as a result, wide dynamic ranges (up to 630) with a high degree of attenuation of nanosecond laser radiation (10-20 times) were achieved. The use of the finite-field DFT method has allowed the calculation of dipole moments, polarizabilities and hyperpolarizabilities. The numerical data obtained during the calculations were used in correlations of theory vs. experiment to derive mathematical expressions (inequalities) to assess the effectiveness of absorbers in limiting the power of laser radiation.

Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon.

Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent. However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and TAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.