Probing of nucleic acid compaction using low-frequency Raman spectroscopy.

Compaction of nucleic acids, namely DNA and RNA, determines their functions and involvement in vital cell processes including transcription, replication, DNA repair and translation. However, experimental probing of the compaction of nucleic acids is not straightforward. In this study, we suggest an approach for this probing using low-frequency Raman spectroscopy. Specifically, we show theoretically, computationally and experimentally the quantifiable correlation between the low-frequency Raman intensity from nucleic acids, magnitude of thermal fluctuations of atomic positions, and the compaction state of biomolecules. Noteworthily, we highlight that the LF Raman intensity differs by an order of magnitude for different samples of DNA, and even for the same sample in the course of long-term storage. The feasibility of the approach is further shown by assessment of the DNA compaction in the nuclei of plant cells. We anticipate that the suggested approach will enlighten compaction of nucleic acids and their dynamics during the key processes of the cell life cycle and under various factors, facilitating advancement of molecular biology and medicine.

Discovery of Clinical Candidate PF-06648671: A Potent γ-Secretase Modulator for the Treatment of Alzheimer's Disease.

Herein, we describe the design and synthesis of γ-secretase modulator (GSM) clinical candidate PF-06648671 (22) for the treatment of Alzheimer's disease. A key component of the design involved a 2,5-cis-tetrahydrofuran (THF) linker to impart conformational rigidity and lock the compound into a putative bioactive conformation. This effort was guided using a pharmacophore model since crystallographic information was not available for the membrane-bound γ-secretase protein complex at the time of this work. PF-06648671 achieved excellent alignment of whole cell in vitro potency (Aß42 IC50 = 9.8 nM) and absorption, distribution, metabolism, and excretion (ADME) parameters. This resulted in favorable in vivo pharmacokinetic (PK) profile in preclinical species, and PF-06648671 achieved a human PK profile suitable for once-a-day dosing. Furthermore, PF-06648671 was found to have favorable brain availability in rodent, which translated into excellent central exposure in human and robust reduction of amyloid ß (Aß) 42 in cerebrospinal fluid (CSF).

Electrostatic Control of Nonlinear Photonic-Crystal Polaritons in a Monolayer Semiconductor.

Integration of 2D semiconductors with photonic crystal slabs provides an attractive approach to achieving strong light-matter coupling and exciton-polariton formation in a chip-compatible geometry. However, for the development of practical devices, it is crucial that polariton excitations are easily tunable and exhibit a strong nonlinear response. Here we study neutral and charged exciton-polaritons in an electrostatically gated photonic crystal slab with an embedded monolayer semiconductor MoSe2 and experimentally demonstrate a novel approach to optical control based on polariton nonlinearity. We show that spatial modulation of the dielectric environment within the photonic crystal unit cell results in the formation of two distinct excitonic species with significantly different nonlinear responses of the corresponding charged exciton-polaritons under optical pumping. This behavior enables optical switching with ultrashort laser pulses and can be sensitively controlled via an electrostatic gate voltage. Our results open new avenues toward the development of active polaritonic devices in a compact chip-compatible implementation.

Characteristics of brain lesions found using MRI imaging in patients with post-COVID with signs of cognitive decline.

OBJECTIVE: Aim: To describe and evaluate abnormalities of the brain in post-COVID patients with neurologic symptoms and cognitive deficits using MRI imaging of the brain. PATIENTS AND METHODS: Materials and Methods: We included 21 patients with a previous positive PCR testing for SARS-CoV-2 and one or more of the following symptoms: memory and cognitive decline, dizziness, anxiety, depression, chronic headaches. All patients had MRI imaging done at onset of symptoms, but after at least 1 year after positive testing for COVID-19 based on the patient's previous medical history. RESULTS: Results: All of the patients complained of lack of concentration, forgetfulness, hard to process information. 15 patients suffered from confusion, 10 from anxiety. Of the 21 patients 14 had isolated chronic headaches, 3 had isolated dizziness, 4 patients had both symptoms upon inclusion. All patients underwent MRI imaging as a part of the diagnostic workup and had varying degrees of neurodegeneration. CONCLUSION: Conclusions: Our data correlates with existing research and shows tendency for cognitive decline in post-COVID patients. This provides groundwork for further research to determine correlation between acceleration of neurodegeneration and post-COVID.

Mn2Ga2S5 and Mn2Al2Se5 van der Waals Chalcogenides: A Source of Atomically Thin Nanomaterials.

Layered chalcogenides containing 3d transition metals are promising for the development of two-dimensional nanomaterials with interesting magnetic properties. Both mechanical and solution-based exfoliation of atomically thin layers is possible due to the low-energy van der Waals bonds. In this paper, we present the synthesis and crystal structures of the Mn2Ga2S5 and Mn2Al2Se5 layered chalcogenides. For Mn2Ga2S5, we report magnetic properties, as well as the exfoliation of nanofilms and nanoscrolls. The synthesis of both polycrystalline phases and single crystals is described, and their chemical stability in air is studied. Crystal structures are probed via powder X-ray diffraction and high-resolution transmission electron microscopy. The new compound Mn2Al2Se5 is isomorphous with Mn2Ga2S5 crystallizing in the Mg2Al2Se5 structure type. The crystal structure is built by the ABCBCA sequence of hexagonal close-packing layers of chalcogen atoms, where Mn2+ and Al3+/Ga3+ species preferentially occupy octahedral and tetrahedral voids, respectively. Mn2Ga2S5 exhibits an antiferromagnetic-like transition at 13 K accompanied by the ferromagnetic hysteresis of magnetization. Significant frustration of the magnetic system may yield spin-glass behavior at low temperatures. The exfoliation of Mn2Ga2S5 layers was performed in a non-polar solvent. Nanolayers and nanoscrolls were observed using high-resolution transmission electron microscopy. Fragments of micron-sized crystallites with a thickness of 70-100 nanometers were deposited on a glass surface, as evidenced by atomic force microscopy.

Rediscovery of mononuclear phagocyte system blockade for nanoparticle drug delivery.

Rapid uptake of nanoparticles by mononuclear phagocyte system (MPS) significantly hampers their therapeutic efficacy. Temporal MPS blockade is one of the few ways to overcome this barrier - the approach rediscovered many times under different names but never extensively used in clinic. Using meta-analysis of the published data we prove the efficacy of this technique for enhancing particle circulation in blood and their delivery to tumours, describe a century of its evolution and potential combined mechanism behind it. Finally, we discuss future directions of the research focusing on the features essential for successful clinical translation of the method.

Correlation between Radical and Quartet State Coherence Times in Photogenerated Triplet-Radical Conjugates.

Molecular quartet states, generated by photoexcitation of chromophore-radical conjugates, have been shown to exhibit attractive properties for applications in the field of molecular spintronics. Many of these applications, such as quantum sensing, require a coherent manipulation of the spin system, implying the need to control the quartet state spin coherence properties. By examining the influence of structural and matrix-related factors, we demonstrate a correlation between the coherence decay of the photogenerated quartet state and that of the tethered stable radical, paving the way for a rational design of photogenerated molecular three-spin systems with optimized coherence properties.

Fluvial carbon dioxide emissions peak at the permafrost thawing front in the Western Siberia Lowland.

In order to foresee the impact of permafrost thaw on CO2 emissions by high-latitude rivers, in-situ measurements across a permafrost and climate/vegetation gradient, coupled with assessment of possible physico-chemical and landscape controlling factors are necessary. Here we chose 34 catchments of variable stream order (1 to 9) and watershed size (1 to >105 km2) located across a permafrost and biome gradient in the Western Siberian Lowland (WSL), from the permafrost-free southern taiga to the continuous permafrost zone of tundra. Across the south-north transect, maximal CO2 emissions (2.2 ± 1.1 g C-CO2 m-2 d-1) occurred from rivers of the discontinuous/sporadic permafrost zone, i.e., geographical permafrost thawing boundary. In this transitional zone, fluvial C emission to downstream export ratio was as high as 8.0, which greatly (x 10) exceeded the ratio in the permafrost free and continuous permafrost zones. Such a high evasion at the permafrost thawing front can stem from an optimal combination of multiple environmental factors: maximal active layer thickness, sizable C stock in soils, and mobilization of labile organic nutrients from dispersed peat ice that enhanced DOC and POC processing in the water column, likely due to priming effect. Via a substituting space for time approach, we foresee an increase in CO2 and CH4 fluvial evasion in the continuous and discontinuous permafrost zone, which is notably linked to the greening of tundra increases in biomass of the riparian vegetation, river water warming and thermokarst lake formation on the watershed.

Dissolved organic matter quality in thermokarst lake water and sediments across a permafrost gradient, Western Siberia.

Thermokarst (thaw) lakes of permafrost peatlands are among the most important sentinels of climate change and sizable contributors of greenhouse gas emissions (GHG) in high latitudes. These lakes are humic, often acidic and exhibit fast growing/drainage depending on the local environmental and permafrost thaw. In contrast to good knowledge of the thermokarst lake water hydrochemistry and GHG fluxes, the sediments pore waters remain virtually unknown, despite the fact that these are hot spots of biogeochemical processes including GHG generation. Towards better understating of dissolved organic matter (DOM) quality at the lake water - sediment interface and in the sediments pore waters, here we studied concentration and optical (UV, visual) properties of DOM of 11 thermokarst lakes located in four permafrost zones of Western Siberia Lowland. We found systematic evaluation of DOM concentration, SUVA and various optical parameters along the vertical profile of lake sediments. The lake size and hence, the stage of lake development, had generally weak control on DOM quality. The permafrost zone exhibited clear impact on DOM porewater concentration, optical characteristics, aromaticity and weight average molecular weight (WAMW). The lowest quality of DOM, reflected in highest SUVA and WAMW, corresponding to the dominance of terrestrial sources, was observed at the southern boundary of the permafrost, in the sporadic/discontinuous zone. This suggests active mobilization of organic matter leachates from the interstitial peat and soil porewaters to the lake, presumably via subsurface or suprapermafrost influx. Applying a substitute space for time scenario for future evolution of OM characteristics in thermokarst lake sediments of Western Siberia, we foresee a decrease of DOM quality, molecular weight and potential bioavailability in lakes of continuous permafrost zone, and an increase in these parameters in the sporadic/discontinuous permafrost zone.

Cholesterol-Modified Anti-Il6 siRNA Reduces the Severity of Acute Lung Injury in Mice.

Small interfering RNA (siRNA) holds significant therapeutic potential by silencing target genes through RNA interference. Current clinical applications of siRNA have been primarily limited to liver diseases, while achievements in delivery methods are expanding their applications to various organs, including the lungs. Cholesterol-conjugated siRNA emerges as a promising delivery approach due to its low toxicity and high efficiency. This study focuses on developing a cholesterol-conjugated anti-Il6 siRNA and the evaluation of its potency for the potential treatment of inflammatory diseases using the example of acute lung injury (ALI). The biological activities of different Il6-targeted siRNAs containing chemical modifications were evaluated in J774 cells in vitro. The lead cholesterol-conjugated anti-Il6 siRNA after intranasal instillation demonstrated dose-dependent therapeutic effects in a mouse model of ALI induced by lipopolysaccharide (LPS). The treatment significantly reduced Il6 mRNA levels, inflammatory cell infiltration, and the severity of lung inflammation. IL6 silencing by cholesterol-conjugated siRNA proves to be a promising strategy for treating inflammatory diseases, with potential applications beyond the lungs.

Toxicological Characteristics of Bacterial Nanocellulose in an In Vivo Experiment-Part 1: The Systemic Effects.

Bacterial nanocellulose (BNC) is being considered as a potential replacement for microcrystalline cellulose as a food additive and a source of dietary fiber due to its unique properties. However, studies on the risks of consuming BNC in food are limited, and it is not yet approved for use in food in the US, EU, and Russia. AIM: This study aims to perform a toxicological and hygienic assessment of the safety of BNC in a subacute 8-week administration in rats. METHODS: BNC was administered to male Wistar rats in doses of 0, 1.0, 10.0, and 100 mg/kg body weight for 8 weeks. Various parameters such as anxiety levels, cognitive function, organ masses, blood serum and liver biochemistry, oxidative stress markers, vitamin levels, antioxidant gene expression, and liver and kidney histology were evaluated. RESULTS: Low and medium doses of BNC increased anxiety levels and liver glutathione, while high doses led to elevated LDL cholesterol, creatinine, and uric acid levels. Liver tissue showed signs of degeneration at high doses. BNC did not significantly affect vitamin levels. CONCLUSION: The adverse effects of BNC are either not dose-dependent or fall within normal physiological ranges. Any effects on rats are likely due to micronutrient deficiencies or impacts on intestinal microbiota.

Annotation of nuclear lncRNAs based on chromatin interactions.

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

Microgravity-like Crystallization of Paramagnetic Species in Strong Magnetic Fields.

The crystallization of paramagnetic species in a magnetic field gradient under microgravity-like conditions is an area of interest for both fundamental and applied science. In this paper, a setup for the crystallization of paramagnetic species in the magnetic field up to 7 T generated by a superconducting magnet is described. The research includes calculations of the conditions necessary to compensate for the gravitational force for several types of paramagnetic substances using the magnetic field of superconducting magnets (4.7 T, 7 T, 9.4 T, and 16.4 T). Additionally, for the first time, the crystallization of copper sulfate and cobalt sulfate, as well as a mixture of copper sulfate and cobalt sulfate under gravitational force compensation in a superconducting magnet, was performed. This paper experimentally demonstrates the feasibility of growing paramagnetic crystals within the volume of a test tube on the example of copper and cobalt sulfate crystals. A comparison of crystals grown from the solution of a mixture of copper and cobalt sulfates under the same conditions, with and without the presence of a magnetic field, showed changes in both the number and size of crystals.

Avoiding common pitfalls in designing kinetic protocols for catalytic amyloid studies.

Kinetic characterization of catalytic amyloids arguably presents a most challenging type of kinetic experiment where careful consideration of many factors is required. Here we outline common pitfalls in devising kinetic studies in such systems. Unlike the more specific protocols for various applications described in this volume, this chapter deals with general issues in setting up kinetic experiments that are incredibly important but often go without explicit mention in the specialized literature. The kinetic fundamentals described here can be also be of use to the enzymologists working with more traditional catalysts.

Screening of oxidative behavior in catalytic amyloid assemblies.

Once considered a thermodynamic minimum of the protein fold or as simply by-products of a misfolding process, amyloids are increasingly showing remarkable potential for promoting enzyme-like catalysis. Recent studies have demonstrated a diverse range of catalytic behaviors that amyloids can promote way beyond the hydrolytic behaviors originally reported. We and others have demonstrated the strong propensity of catalytic amyloids to facilitate redox reactions both in the presence and in the absence of metal cofactors. Here, we present a detailed protocol for measuring the oxidative ability of supramolecular peptide assemblies.

Computational modelling of supramolecular metallopeptide assemblies.

Among the important questions in supramolecular peptide self-assemblies are their interactions with metallic compounds and ions. In the last decade, intensive efforts have been devoted to understanding the structural properties of these interactions including their dynamical and catalytic impact in natural and de novo systems. Since structural insights from experimental approaches could be particularly challenging, computational chemistry methods are interesting complementary tools. Here, we present the general multiscale strategies we developed and applied for the study of metallopeptide assemblies. These strategies include prediction of metal binding site, docking of metallic moieties, classical and accelerated molecular dynamics and finally QM/MM calculations. The systems of choice for this chapter are, on one side, peptides involved in neurodegenerative diseases and, on the other, de novo fibrillar systems with catalytic properties. Both successes and remaining challenges are highlighted so that the protocol could be apply to other system of this kind.

Structural and Immunological Features of PR-10 Allergens: Focusing on the Major Alder Pollen Allergen Aln g 1.

Today, allergies have become a serious problem. PR-10 proteins are clinically relevant allergens that have the ability to bind hydrophobic ligands, which can significantly increase their allergenicity potential. It has been recently shown that not only the birch pollen allergen Bet v 1 but also the alder pollen allergen Aln g 1, might act as a true sensitizer of the immune system. The current investigation is aimed at the further study of the allergenic and structural features of Aln g 1. By using qPCR, we showed that Aln g 1 was able to upregulate alarmins in epithelial cells, playing an important role in sensitization. With the use of CD-spectroscopy and ELISA assays with the sera of allergic patients, we demonstrated that Aln g 1 did not completely restore its structure after thermal denaturation, which led to a decrease in its IgE-binding capacity. Using site-directed mutagenesis, we revealed that the replacement of two residues (Asp27 and Leu30) in the structure of Aln g 1 led to a decrease in its ability to bind to both IgE from sera of allergic patients and lipid ligands. The obtained data open a prospect for the development of hypoallergenic variants of the major alder allergen Aln g 1 for allergen-specific immunotherapy.

Signatures of epigenetic, biological and mitotic age acceleration and telomere shortening are associated with arsenic-induced skin lesions.

Chronic arsenic exposure is a global health hazard significantly associated with the development of deleterious cutaneous changes and increased keratinocyte cancer risk. Although arsenic exposure is associated with broad-scale cellular and molecular changes, gaps exist in understanding how these changes impact the skin and facilitate malignant transformation. Recently developed epigenetic "clocks" can accurately predict chronological, biological and mitotic age, as well as telomere length, on the basis of tissue DNA methylation state. Deviations of predicted from expected age (epigenetic age dysregulation) have been associated with numerous complex diseases, increased all-cause mortality and higher cancer risk. We investigated the ability of these algorithms to detect molecular changes associated with chronic arsenic exposure in the context of associated skin lesions. To accomplish this, we utilized a multi-algorithmic approach incorporating seven "clocks" (Horvath, Skin&Blood, PhenoAge, PCPhenoAge, GrimAge, DNAmTL and epiTOC2) to analyze peripheral blood of pediatric and adult cohorts of arsenic-exposed (n = 84) and arsenic-naïve (n = 33) individuals, among whom n = 18 were affected by skin lesions. Arsenic-exposed adults with skin lesions exhibited accelerated epigenetic (Skin&Blood: + 7.0 years [95% CI 3.7; 10.2], q = 6.8 × 10-4), biological (PhenoAge: + 5.8 years [95% CI 0.7; 11.0], q = 7.4 × 10-2, p = 2.8 × 10-2) and mitotic age (epiTOC2: + 19.7 annual cell divisions [95% CI 1.8; 37.7], q = 7.4 × 10-2, p = 3.2 × 10-2) compared to healthy arsenic-naïve individuals; and accelerated epigenetic age (Skin&Blood: + 2.8 years [95% CI 0.2; 5.3], q = 2.4 × 10-1, p = 3.4 × 10-2) compared to lesion-free arsenic-exposed individuals. Moreover, lesion-free exposed adults exhibited accelerated Skin&Blood age (+ 4.2 [95% CI 1.3; 7.1], q = 3.8 × 10-2) compared to their arsenic-naïve counterparts. Compared to the pediatric group, arsenic-exposed adults exhibited accelerated epigenetic (+ 3.1 to 4.4 years (95% CI 1.2; 6.4], q = 2.4 × 10-4-3.1 × 10-3), biological (+ 7.4 to 7.8 years [95% CI 3.0; 12.1] q = 1.6 × 10-3-2.8 × 10-3) and mitotic age (+ 50.0 annual cell divisions [95% CI 15.6; 84.5], q = 7.8 × 10-3), as well as shortened telomere length (- 0.23 kilobases [95% CI - 0.13; - 0.33], q = 2.4 × 10-4), across all seven algorithms. We demonstrate that lifetime arsenic exposure and presence of arsenic-associated skin lesions are associated with accelerated epigenetic, biological and mitotic age, and shortened telomere length, reflecting altered immune signaling and genomic regulation. Our findings highlight the usefulness of DNA methylation-based algorithms in identifying deleterious molecular changes associated with chronic exposure to the heavy metal, serving as potential prognosticators of arsenic-induced cutaneous malignancy.