Dual-Omics Approach Unveils Novel Perspective on the Quality Control of Genetically Engineered Exosomes.

Exosomes, nanoscale vesicles derived from human cells, offer great promise for targeted drug delivery. However, their inherent diversity and genetic modifications present challenges in terms of ensuring quality in clinical use. To explore solutions, we employed advanced gene fusion and transfection techniques in human 293T cells to generate two distinct sets of genetically engineered samples. We used dual-omics analysis, combining transcriptomics and proteomics, to comprehensively assess exosome quality by comparing with controls. Transcriptomic profiling showed increased levels of engineering scaffolds in the modified groups, confirming the success of genetic manipulation. Through transcriptomic analysis, we identified 15 RNA species, including 2008 miRNAs and 13,897 mRNAs, loaded onto exosomes, with no significant differences in miRNA or mRNA levels between the control and engineered exosomes. Proteomics analysis identified changes introduced through genetic engineering and over 1330 endogenous exosome-associated proteins, indicating the complex nature of the samples. Further pathway analysis showed enrichment in a small subset of cellular signaling pathways, aiding in our understanding of the potential biological impacts on recipient cells. Detection of over 100 cow proteins highlighted the effectiveness of LC-MS for identifying potential contaminants. Our findings establish a dual-omics framework for the quality control of engineered exosome products, facilitating their clinical translation and therapeutic applications in nanomedicine.

Fast switching between the ground- and excited-state lasing in a quantum-dot microdisk triggered by sub-ps pulses.

A quantum-dot microdisk was optically pumped by continuous-wave excitation with a level sufficient for the ground-state lasing. The microdisk was additionally illuminated with sub-ps pulses of various powers. It was found that there is a critical level of pulse power that determines the subsequent transient process of the microlaser. Depending on the level of the pulsed excitation, the ground-state lasing intensity can be either enhanced (for weak pulses) or fully quenched (for strong pulses). In the latter case, the excited-state lasing is ignited for a short time. All dynamic phenomena occur on a time scale of the order of 100 ps, and the duration of the transient process as a whole (from the arrival of the excitation pulse to the restoration of steady-state intensities) lasts no more than 0.5 ns. Using this phenomenon, a microlaser can be rapidly switched between two states with the switching controlled by the level of the incoming optical pulse.

Rapid and Simple 13C-Hyperpolarization by 1H Dissolution Dynamic Nuclear Polarization Followed by an Inline Magnetic Field Inversion.

Dissolution dynamic nuclear polarization (dDNP) is a method of choice for preparing hyperpolarized 13C metabolites such as 1-13C-pyruvate used for in vivo applications, including the real-time monitoring of cancer cell metabolism in human patients. The approach consists of transferring the high polarization of electron spins to nuclear spins via microwave irradiation at low temperatures (1.0-1.5 K) and moderate magnetic fields (3.3-7 T). The solid sample is then dissolved and transferred to an NMR spectrometer or MRI scanner for detection in the liquid state. Common dDNP protocols use direct hyperpolarization of 13C spins reaching polarizations of >50% in ∼1-2 h. Alternatively, 1H spins are polarized before transferring their polarization to 13C spins using cross-polarization, reaching polarization levels similar to those of direct DNP in only ∼20 min. However, it relies on more complex instrumentation, requiring highly skilled personnel. Here, we explore an alternative route using 1H dDNP followed by inline adiabatic magnetic field inversion in the liquid state during the transfer. 1H polarizations of >70% in the solid state are obtained in ∼5-10 min. As the hyperpolarized sample travels from the dDNP polarizer to the NMR spectrometer, it goes through a field inversion chamber, which causes the 1H → 13C polarization transfer. This transfer is made possible by the J-coupling between the heteronuclei, which mixes the Zeeman states at zero-field and causes an antilevel crossing. We report liquid-state 13C polarization up to ∼17% for 3-13C-pyruvate and 13C-formate. The instrumentation needed to perform this experiment in addition to a conventional dDNP polarizer is simple and readily assembled.

Isolation of High-Molecular-Weight DNA for Long-Read Sequencing Using a High-Salt Gel Electroelution Trap.

Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW DNA that takes advantage of the fact that DNA's electrophoretic mobility decreases in a high-ionic-strength environment. The method begins with the separation of HMW DNA from various impurities by electrophoresis in an agarose gel-filled channel. After sufficient separation, a high-salt gel block is placed ahead of the DNA band of interest, leaving a gap between the separating gel and the high-salt gel that serves as a reservoir for sample collection. The DNA is then electroeluted from the separating gel into the reservoir, where its migration slows due to electrostatic shielding of the DNA's negative charge by excess counterions from the high-salt gel. As a result, the reservoir accumulates HMW DNA of high purity and integrity, which can be easily collected and used for long-read sequencing and other demanding applications without additional desalting. The method is simple and inexpensive, yields sequencing-grade HMW DNA even from difficult plant and soil samples, and has the potential for automation and scalability.

Expression, Intracellular Localization, and Maturation of Cysteine Cathepsins in Renal Embryonic and Cancer Cell Lines.

Cysteine cathepsins play an important role in tumor development and metastasis. The expression of these enzymes is often increased in many types of tumor cells. Cysteine cathepsins contribute to carcinogenesis through a number of mechanisms, including proteolysis of extracellular matrix and signaling molecules on the cell surface, as well as degradation of transcription factors and disruption of signaling cascades in the cell nucleus. Distinct oncogenic functions have been reported for several members of the cysteine cathepsin family in various types of cancer, but a comparative study of all eleven cysteine cathepsins in one experimental model is still missing. In this work, we assessed and compared the expression, localization, and maturation of all eleven cysteine cathepsins in embryonic kidney cells HEK293 and kidney cancer cell lines 769-P and A-498. We found that the expression of cathepsins V, B, Z, L, and S was 3- to 9-fold higher in kidney tumor cells than in embryonic cells. We also showed that all cysteine cathepsins were present in varying amounts in the nucleus of both embryonic and tumor cells. Notably, more than half of the cathepsin Z or K and over 88% of cathepsin F were localized in tumor cell nuclei. Moreover, mature forms of cysteine cathepsins were more prevalent in tumor cells than in embryonic cells. These results can be further used to develop novel diagnostic tools and may assist in the investigation of cysteine cathepsins as potential therapeutic targets.

The emerging roles of long noncoding RNAs in lymphatic vascular development and disease.

Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.

Construction of Annulated Spiro[4.4]-nonane-diones via the Tandem [4 + 2]-Cycloaddition/Aromatization Reaction.

A method for the synthesis of both symmetric and asymmetric fused spiro[4.4]-nonane-dione derivatives has been developed. It is based on a Diels-Alder reaction of spiro[4.4]nona-2,7-diene-1,6-dione as a dienophile component followed by immediate aromatization of the adduct. An active diene component can be generated using the tetrabromoxylene/NaI system, the 1,3-diphenylisobenzofuran/BF3 system, or substituted cyclones.

Two-state lasing in a quantum dot racetrack microlaser.

The peculiarities of two-state lasing in a racetrack microlaser with an InAs/GaAs quantum dot active region are investigated by measuring the electroluminescence spectra at various injection currents and temperatures. Unlike edge-emitting and microdisk lasers, where two-state lasing involves the ground and first excited-state optical transitions of quantum dots, in racetrack microlasers, we observe lasing through the ground and second excited states. As a result, the spectral separation between lasing bands is doubled to more than 150 nm. A temperature dependence of threshold currents for lasing via ground and second excited states of quantum dots was also obtained.

Potent dual MAGL/FAAH inhibitor AKU-005 engages endocannabinoids to diminish meningeal nociception implicated in migraine pain.

BACKGROUND: Engaging the endocannabinoid system through inhibition of monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH), degrading endocannabinoids (endoCBs) 2-arachidonoylglycerol (2-AG) and anandamide (AEA), was proposed as a promising approach to ameliorate migraine pain. However, the activity of MAGL and FAAH and action of endoCB on spiking activity of meningeal afferents, from which migraine pain originates, has not been explored thus far. Therefore, we here explored the analgesic effects of endoCB enhancement in rat and human meningeal tissues. METHODS: Both MAGL and FAAH activity and local 2-AG and AEA levels were measured by activity-based protein profiling (ABPP) and LC-MS/MS, respectively, in rat meninges obtained from hemiskulls of P38-P40 Wistar rats and human meninges from elderly patients undergoing non-migraine related neurosurgery. The action on endoCBs upon administration of novel dual MAGL/FAAH inhibitor AKU-005 on meningeal afferents excitability was tested by investigating paired KCl-induced spiking and validation with local (co-)application of either AEA or 2-AG. Finally, the specific TRPV1 agonist capsaicin and blocker capsazepine were tested. RESULTS: The basal level of 2-AG exceeded that of AEA in rat and human meninges. KCl-induced depolarization doubled the level of AEA. AKU-005 slightly increased spontaneous spiking activity whereas the dual MAGL/FAAH inhibitor significantly decreased excitation of nerve fibres induced by KCl. Similar inhibitory effects on meningeal afferents were observed with local applications of 2-AG or AEA. The action of AKU-005 was reversed by CB1 antagonist AM-251, implying CB1 receptor involvement in the anti-nociceptive effect. The inhibitory action of AEA was also reversed by AM-251, but not with the TRPV1 antagonist capsazepine. Data cluster analysis revealed that both AKU-005 and AEA largely increased long-term depression-like meningeal spiking activity upon paired KCl-induced spiking. CONCLUSIONS: In the meninges, high anti-nociceptive 2-AG levels can tonically counteract meningeal signalling, whereas AEA can be engaged on demand by local depolarization. AEA-mediated anti-nociceptive effects through CB1 receptors have therapeutic potential. Together with previously detected MAGL activity in trigeminal ganglia, dual MAGL/FAAH inhibitor AKU-005 appears promising as migraine treatment.

Temperature Evolution of Two-State Lasing in Microdisk Lasers with InAs/InGaAs Quantum Dots.

One-state and two-state lasing is investigated experimentally and through numerical simulation as a function of temperature in microdisk lasers with Stranski-Krastanow InAs/InGaAs/GaAs quantum dots. Near room temperature, the temperature-induced increment of the ground-state threshold current density is relatively weak and can be described by a characteristic temperature of about 150 K. At elevated temperatures, a faster (super-exponential) increase in the threshold current density is observed. Meanwhile, the current density corresponding to the onset of two-state lasing was found to decrease with increasing temperature, so that the interval of current density of pure one-state lasing becomes narrower with the temperature increase. Above a certain critical temperature, ground-state lasing completely disappears. This critical temperature drops from 107 to 37 °C as the microdisk diameter decreases from 28 to 20 µm. In microdisks with a diameter of 9 µm, a temperature-induced jump in the lasing wavelength from the first excited-state to second excited-state optical transition is observed. A model describing the system of rate equations and free carrier absorption dependent on the reservoir population provides a satisfactory agreement with experimental results. The temperature and threshold current corresponding to the quenching of ground-state lasing can be well approximated by linear functions of saturated gain and output loss.

Heavily Gd-Doped Non-Toxic Cerium Oxide Nanoparticles for MRI Labelling of Stem Cells.

Recently, human mesenchymal stem cells (hMSc) have attracted a great deal of attention as potential therapeutic agents in the treatment of socially significant diseases. Despite substantial advances in stem-cell therapy, the biological mechanisms of hMSc action after transplantation remain unclear. The use of magnetic resonance imaging (MRI) as a non-invasive method for tracking stem cells in the body is very important for analysing their distribution in tissues and organs, as well as for ensuring control of their lifetime after injection. Herein, detailed experimental data are reported on the biocompatibility towards hMSc of heavily gadolinium-doped cerium oxide nanoparticles (Ce0.8Gd0.2O2-x) synthesised using two synthetic protocols. The relaxivity of the nanoparticles was measured in a magnetic field range from 1 mT to 16.4 T. The relaxivity values (r1 = 11 ± 1.2 mM-1 s-1 and r1 = 7 ± 1.2 mM-1 s-1 in magnetic fields typical of 1.5 and 3 T MRI scanners, respectively) are considerably higher than those of the commercial Omniscan MRI contrast agent. The low toxicity of gadolinium-doped ceria nanoparticles to hMSc enables their use as an effective theranostic tool with improved MRI-contrasting properties.

Features of the Macro-, Micro-, and Fine Structure of the Nickel Superalloy Product Material Formed by the Method of Electron Beam Additive Manufacturing.

In the present work, the products in the form of vertical walls were made of heat-resistant nickel-based superalloy ZhS32 via the method of electron beam additive technology. Unidirectional printing strategy was applied. The effect of heat input and 3D printing strategy on the macrostructure, dimensions, and morphology of microstructure elements was established. It was shown that the additive product material has a directed macrostructure. The only exclusion was the final layer with a thickness of no more than 3.5 mm. The directed macrostructure consisted of dendrites oriented predominantly along the crystallographic direction {001} of the primary dendrite arms. The misorientation of the dendrite axes did not exceed 9 degrees. The angle between the predominant dendrite growth direction and the normal to the substrate was 23 degrees. The average primary dendrite arms' spacing increased monotonically from 16 µm at 5 mm from the substrate to 23 µm in the final layers of the product material (the overall height was 41 mm). It was found that the average size of γ' (Ni3Al)-phase precipitations in the form of nanoscale and submicrocrystalline cuboids varied in the range of 76 to 163 nm depending on the distance from the substrate. The size of γ'-phase precipitations reached a maximum at about 30 mm from the substrate, while in the final layers of the product material, the average cuboid size did not exceed 135 nm. Extreme dependence of the size of γ'-phase precipitations on the height of the product followed from a combination of a given monotonic decrease in heat input and heat accumulation in the product material as it formed, as did additional heat removal by means of radiation during formation of the final layer of the product without re-melting. Chemical elements of the austenitic steel substrate material were not detected in the product material more than 8 mm from the substrate. There were no macrodefects, such as voids, in the entire volume of the product material.

Analytical solution for the inverting pulses with constant adiabaticity.

The exact solution was found for inverting pulses with constant adiabaticity for spin ½. The analytical relationship between the time-varying frequency of the microwave resonant field (or RF field in the case of NMR) and its amplitude time dependence such that the adiabaticity parameter remains constant for the single isochromat throughout the pulse is found. Comparison with EPR (hyperbolic tangent)-(hyperbolic secant) pulse method was carried out. On the basis of the analytical solution the pulses with different dependences of the microwave field amplitude conserving the constant adiabaticity have been constructed. The pulses exhibit rather sharp inversion selectivity that can be used in the field of EPR, NMR and MRI.

P2O5-Promoted Cyclization of Di[aryl(hetaryl)methyl] Malonic Acids as a Pathway to Fused Spiro[4.4]nonane-1,6-Diones.

Conventional spiro-linked conjugated materials are attractive for organic optoelectronic applications due to the unique combination of their optical and electronic properties. However, spiro-linked conjugated materials with conjugation extension directed along the main axis of the molecule are still only rare examples among the vast number of spiro-linked conjugated materials. Herein, the synthesis, leading to π-extended spiro-linked conjugated materials─spiro[4.4]nonane-1,6-diones and spiro[5.5]undecane-1,7-diones─has been developed and optimized. The proposed design concept starts from readily available malonic esters and contains several steps: double alkylation of malonic ester with bromomethylaryl(hetaryl)s; conversion of a malonic ester into the corresponding malonic acid; electrophilic spirocyclization of the latter into the annulated spiro[4.4]nonane-1,6-dione or spiro[5.5]undecane-1,7-dione in the presence of phosphorus pentoxide. On the basis of these insights, the developed method yielded spiro-linked conjugated cores fused with benzene, thiophene, and naphthalene, decorated with active halogen atoms. The structures of the synthesized spirocycles were determined by single-crystal X-ray diffraction analysis. Benzene fused spiro[4.4]nonane-1,6-dione decorated with bromine atoms was transformed into V-shape phenylene-thiophene co-oligomer type spirodimers via Stille coupling. The spiro-bis(4-n-dodecylphenyl)-2,2'-bithiophene derivative possessed high photoluminescence properties in both solution and solid state with a photoluminescence quantum yield (PL QY) of 38%.

16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients.

The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism. This data article describes the microbiome dataset from the upper respiratory tract of SARS-CoV-2 positive patients from Russia. This dataset reports the microbial community profile of 335 human nasopharyngeal swabs collected between 2020-05 and 2021-03 during the first and the second epidemic waves. Samples were collected from both inpatients and outpatients in 4 cities of the Russian Federation (Moscow, Kazan, Irkutsk, Nizhny Novgorod) and sequenced using the 16S rRNA gene amplicon sequencing of V3-V4 region. Data contains information about the patient such as age, sex, hospitalization status, percent of damaged lung tissue, oxygen saturation (SpO2), respiratory rate, need for supplemental oxygen, chest computer tomography severity score, SARS-CoV-2 lineage, and also information about smoking and comorbidities. The amplicon sequencing data were deposited at NCBI SRA as BioProject PRJNA751478.

Photo-CIDNP in Solid State.

Photo-CIDNP (photo-chemically induced dynamic nuclear polarization) refers to nuclear polarization created by the spin-chemical evolution of spin-correlated radical pairs (SCRPs). This phenomenon occurs in gases, liquids and solids. Based on the solid-state photo-CIDNP effect observed under magic-angle spinning (MAS), photo-CIDNP MAS NMR has been developed as analytical method. Here we report the origin, the theory and the state of the art of this method.

Floquet theory in magnetic resonance: Formalism and applications.

Floquet theory is an elegant mathematical formalism originally developed to solve time-dependent differential equations. Besides other fields, it has found applications in optical spectroscopy and nuclear magnetic resonance (NMR). This review attempts to give a perspective of the Floquet formalism as applied in NMR and shows how it allows one to solve various problems with a focus on solid-state NMR. We include both matrix- and operator-based approaches. We discuss different problems where the Hamiltonian changes with time in a periodic way. Such situations occur, for example, in solid-state NMR experiments where the time dependence of the Hamiltonian originates either from magic-angle spinning or from the application of amplitude- or phase-modulated radiofrequency fields, or from both. Specific cases include multiple-quantum and multiple-frequency excitation schemes. In all these cases, Floquet analysis allows one to define an effective Hamiltonian and, moreover, to treat cases that cannot be described by the more popularly used and simpler-looking average Hamiltonian theory based on the Magnus expansion. An important example is given by spin dynamics originating from multiple-quantum phenomena (level crossings). We show that the Floquet formalism is a very general approach for solving diverse problems in spectroscopy.

Nuclear singlet relaxation by chemical exchange.

The population imbalance between nuclear singlet states and triplet states of strongly coupled spin-1/2 pairs, also known as nuclear singlet order, is well protected against several common relaxation mechanisms. We study the nuclear singlet relaxation of 13C pairs in aqueous solutions of 1,2-13C2 squarate over a range of pH values. The 13C singlet order is accessed by introducing 18O nuclei in order to break the chemical equivalence. The squarate dianion is in chemical equilibrium with hydrogen-squarate (SqH-) and squaric acid (SqH2) characterized by the dissociation constants pK1 = 1.5 and pK2 = 3.4. Surprisingly, we observe a striking increase in the singlet decay time constants TS when the pH of the solution exceeds ∼10, which is far above the acid-base equilibrium points. We derive general rate expressions for chemical-exchange-induced nuclear singlet relaxation and provide a qualitative explanation of the TS behavior of the squarate dianion. We identify a kinetic contribution to the singlet relaxation rate constant, which explicitly depends on kinetic rate constants. Qualitative agreement is achieved between the theory and the experimental data. This study shows that infrequent chemical events may have a strong effect on the relaxation of nuclear singlet order.

Singlet to triplet conversion in molecular hydrogen and its role in parahydrogen induced polarization.

Detailed experimental and comprehensive theoretical analysis of singlet-triplet conversion in molecular hydrogen dissolved in a solution together with organometallic complexes used in experiments with parahydrogen (the H2 molecule in its nuclear singlet spin state) is reported. We demonstrate that this conversion, which gives rise to formation of orthohydrogen (the H2 molecule in its nuclear triplet spin state), is a remarkably efficient process that strongly reduces the resulting NMR (nuclear magnetic resonance) signal enhancement, here of 15N nuclei polarized at high fields using suitable NMR pulse sequences. We make use of a simple improvement of traditional pulse sequences, utilizing a single pulse on the proton channel that gives rise to an additional strong increase of the signal. Furthermore, analysis of the enhancement as a function of the pulse length allows one to estimate the actual population of the spin states of H2. We are also able to demonstrate that the spin conversion process in H2 is strongly affected by the concentration of 15N nuclei. This observation allows us to explain the dependence of the 15N signal enhancement on the abundance of 15N isotopes.

Simultaneous 15 N polarization of several biocompatible substrates in ethanol-water mixtures by signal amplification by reversible exchange (SABRE) method.

Signal amplification by reversible exchange (SABRE) is a popular method for generating strong signal enhancements in nuclear magnetic resonance (NMR). In SABRE experiments, the source of polarization is provided by the nonthermal spin order of parahydrogen (pH2 , the H2 molecule in its nuclear singlet spin state). Polarization formation requires that both pH2 and a substrate molecule bind to an Ir-based complex where polarization transfer occurs. Subsequently, the complex dissociates and free polarized substrate molecules are formed. In this work, we present approaches towards biocompatible SABRE, meaning that several small biomolecules are simultaneously polarized by using the SABRE method in water-ethanol solutions at room temperature. We are able to demonstrate significant 15 N-NMR signal enhancements in water-ethanol solutions for biomolecules like nicotinamide, metronidazole, adenosine-5'-monophosphate, and 4-methylimidazole and found that the first three substrates are polarized at the same level as a well-known pyridine. We show that simultaneous polarization of several molecules is indeed feasible when the reactions are carried out at an ultralow field of about 400-500 nT. The achieved enhancements are between 100-fold and 15,000-fold. The resulting 15 N polarization (maximal value about 4% achieved for metronidazole and pyridine at 45°C) strongly depends on the sample temperature, pH2 bubbling pressure, and pH2 flow. One more parameter, which is important for optimizing the enhancement, is the solvent pH. Hence, this study presents a step in developing biocompatible SABRE polarization and gives a clue on how such SABRE experiments should be optimized to achieve the highest NMR signal enhancement.