Thermodynamic parameters obtained for the formation of the Cas12a-RNA/DNA complex.

The thermodynamics of interactions between Cas12a, RNA, and DNA are important to understanding the molecular mechanisms governing CRISPR-Cas12a's specificity and function. In this study, we employed isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations to investigate the binding properties and energetic contributions of Cas12a-crRNA complexes with single-stranded (ssDNA) and double-stranded (dsDNA) DNA substrates. ITC analyses revealed significant thermal effects during the interaction of Cas12a-crRNA with ssDNA but no detectable effects with dsDNA.

Homoplasy in the embryonic development of terrestrial and epiphytic orchids from the subtribe Malaxidinae (Orchidaceae).

During evolution, similar vectors of adaptive radiation may have evolved in the subtribe Malaxidinae. This was manifested in homologous series of variability in suspensor shape and seed coat ultrasculpture in clades of terrestrial and epiphytic orchids. The present study examines the variability of embryonic traits across clades and subclades of subtribe Malaxidinae (Orchidaceae), previously identified by molecular genetic data.

Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features.

The non-ideal accuracy and insufficient selectivity of CRISPR/Cas9 systems is a serious problem for their use as a genome editing tool. It is important to select the target sequence correctly so that the CRISPR/Cas9 system does not cut similar sequences. This requires an understanding of how and why mismatches in the target sequence can affect the efficiency of the Cas9/sgRNA complex.

Redox Transformations of the OX063 Radical in Biological Media: Oxidative Decay of Initial Trityl with Further Formation of Structurally-Modified TAM.

Being a low-toxic and hydrophilic representative of TAM, OX063 has shown its suitability for in-vivo and in-cell EPR experiments and design of spin labels. Using C labeling, we investigated the course of oxidative degradation of OX063 into quinone-methide (QM) under the influence of superoxide as well as further thiol-promoted reduction of QM into TAM radical, which formally corresponds to substitution of a carboxyl function by a hydroxyl group. We found these transformations being quantitative in model reactions mimicking specific features of biological media and confirmed the presence of these reactions in the blood and liver homogenate of mice in vitro.

Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase.

8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells.

Untargeted Plasma Metabolomic Profiling in Patients with Depressive Disorders: A Preliminary Study.

Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work was a metabolomic analysis of blood serum to classify patients with depressive disorders and healthy individuals using Compound Discoverer software.

Microstructure evolution and the deformation mechanism in nanocrystalline superior-deformed tantalum.

The temperature-controlled relationship between the mechanical properties and deformation mechanism of tantalum (Ta) enables the extension of its application potential in various areas of life, including energy and electronics industries. In this work, the microstructure and deformation behavior of nanocrystalline superior-deformed Ta have been investigated in a wide temperature range. The structural analysis revealed that the high-performance Ta consists of several different substructures, with an average size of about 20 nm.

The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA.

Non-heme dioxygenases of the AlkB family hold a unique position among enzymes that repair alkyl lesions in nucleic acids. These enzymes activate the Fe(II) ion and molecular oxygen through the coupled decarboxylation of the 2-oxoglutarate co-substrate to subsequently oxidize the substrate. ALKBH3 is a human homolog of AlkB, which displays a specific activity toward N1-methyladenine and N3-methylcytosine bases in single-stranded DNA.

Chemical Composition of Methanol Extracts from Leaves and Flowers of (Ranunculaceae).

Siebold et Zucc. is an unstudied single-species genus belonging to the tribe Cimicifugeae (Ranunculaceae). The only species of this genus- Siebold and Zucc.

Megasporogenesis, megagametogenesis and embryogenesis of Liparis elliptica (Orchidaceae), with special note to the development of unique unitegmal ovule.

Megasporogenesis, megagametogenesis and embryogenesis of Liparis elliptica (family Orchidaceae, tribe Malaxideae, subtribe Malaxidinae) have been studied. It was shown that the L. elliptica embryo sac is monosporic and develops from the chalazal cell of the megaspore triad according to the modified Polygonum type.

Non-Targeted Screening of Metabolites in Aqueous-Ethanol Extract from (Rosaceae) Using LC-HRMS.

By means of liquid chromatography combined with high-resolution mass spectrometry, metabolite profiling was performed on an aqueous-ethanol extract from (Rosaceae) collected in Siberia (Russia). Up to 140 compounds were found in the extract, of which 47 were tentatively identified. The identified compounds were amino acids, sugars, phenylpropanoids, fatty acids and their derivatives, triterpenoids, flavonoids, and others.

Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases.

Apurinic/apyrimidinic (AP) sites are abundant DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and as base excision repair (BER) intermediates. AP sites and their derivatives readily trap DNA-bound proteins, resulting in DNA-protein cross-links. Those are subject to proteolysis but the fate of the resulting AP-peptide cross-links (APPXLs) is unclear.

Geochemical ceramic composition dataset using neutron activation and statistical analyses.

These are comprehensive baseline data on the geochemical composition of archeological ceramics analyzed using instrumental neutron activation analysis (INAA). The data obtained support the research article conducted to evaluate the elemental composition of 70 sherds that were collected from different locations [1], [2], [3]. The mass fractions in wt% and in mg/kg of 39 oxides and elements were determined, respectively.

LC-HRMS for the Identification of Quercetin and Its Derivatives in (Rosaceae) and Anatomical Features of Its Leaves.

L. is affiliated with the section Ser. of the genus L.

Achieving Ultrahigh Energy Storage Density of La and Ta Codoped AgNbO Ceramics by Optimizing the Field-Induced Phase Transitions.

Energy storage capacitors are extensively used in pulsed power devices because of fast charge/discharge rates and high power density. However, the low energy storage density and efficiency of dielectric capacitors limit their further commercialization in modern energy storage applications. Lead-free AgNbO-based antiferroelectric (AFE) ceramics are considered to be one of the most promising environmentally friendly materials for dielectric capacitors because of their characteristic double polarization-electric field hysteresis loops with small remanent polarization and large maximum polarization.

Structure- and Content-Dependent Efficiency of Cas9-Assisted DNA Cleavage in Genome-Editing Systems.

Genome-editing systems, being some of the key tools of molecular biologists, represent a reasonable hope for progress in the field of personalized medicine. A major problem with such systems is their nonideal accuracy and insufficient selectivity. The selectivity of CRISPR-Cas9 systems can be improved in several ways.

Terahertz Faraday Rotation of SrFeO Hexaferrites Enhanced by Nb Doping.

The magneto-optical and dielectric behavior of M-type hexaferrites as permanent magnets in the THz band is essential for potential applications like microwave absorbers and antennas, while are rarely reported in recent years. In this work, single-phase SrFeNbO hexaferrite ceramics were prepared by the conventional solid-state sintering method. Temperature dependence of dielectric parameters was investigated here to determine the relationship between dielectric response and magnetic phase transition.

Thermodynamic Swings: How Ideal Complex of Cas9-RNA/DNA Forms.

Most processes of the recognition and formation of specific complexes in living systems begin with collisions in solutions or quasi-solutions. Then, the thermodynamic regulation of complex formation and fine tuning of complexes come into play. Precise regulation is very important in all cellular processes, including genome editing using the CRISPR-Cas9 tool.

Application of Parallel Reaction Monitoring to the Development and Validation of a Quantitative Assay for ST-246 in Human Plasma.

In this work, we developed and validated a robust and sensitive method of liquid chromatography with high-resolution mass spectrometry in parallel reaction monitoring (PRM) mode for ST-246 (tecovirimat) quantification in human blood plasma. The method was compared with the multiple reaction monitoring (MRM) technique and showed better selectivity and similar sensitivity in a wider concentration range (10-5000 ng/mL). Within this range, intra- and interday variability of precision and accuracy were within acceptable ranges in accordance with the European Medicines Agency guidelines, and recovery was 87.

Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance.

DNA polymerases β (Pol β) and λ (Pol λ) belong to one structural family (X family) and possess the same enzymatic activities. Nonetheless, these enzymes have differences in their catalytic efficiency and specificity. We have previously reported that these enzymes can bypass bulky benzo[a]pyrene-DNA adducts via translesion synthesis during gap-filling reactions, although efficiency and specificity are dependent on the reaction conditions and adduct conformation.

Development and Validation of a Method of Liquid Chromatography Coupled with Tandem Mass Spectrometry for Quantification of ST-246 (Tecovirimat) in Human Plasma.

The aim of this work was to develop and validate a sensitive and robust method of liquid chromatography coupled with tandem mass spectrometry to quantitate ST-246 (tecovirimat) in plasma using an internal standard (2-hydroxy-N-{3,5-dioxo-4-azatetracyclo [5.3.2.

Probing the Dynamics of Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry.

The Cas9 endonuclease is an essential component of the CRISPR-Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR-Cas9 system. A deep understanding of the Cas9 mechanism and its structural-functional relationships is required to develop strategies for precise gene editing.

Dataset for dynamics and conformational changes in human NEIL2 protein analyzed by integrative structural biology approach.

This work presents new data on human endonuclease VIII-like 2 protein (hNEIL2), a part of DNA glycosylases of the helix-two-turn-helix structural superfamily. While X-ray structure of oNEIL2 (opossum Monodelphis) was resolved partially [1], the structure of hNEIL2 has not yet been determined. This data article describes a powerful combination of hydrogen-deuterium exchange mass spectrometry, homology modeling, and molecular dynamics simulations for protein conformational dynamics analysis.

Grain Size Effects in Mn-Modified 0.67BiFeO-0.33BaTiO Ceramics.

Grain size can have significant effects on the properties of electroceramics for dielectric, piezoelectric, and ferroelectric applications. Here, we systematically investigate the effect of grain size on the structure and properties of Mn-modified 0.67BiFeO-0.