Molecular Mapping Research Articles

Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer

Breast cancer is one of the prevailing cancers globally, with a high mortality rate. Metastatic breast cancer (MBC) is an advanced stage of cancer, characterised by a highly nonlinear, heterogeneous process involving numerous singling pathways and regulatory interactions. Epithelial–mesenchymal transition (EMT) emerges as a key mechanism exploited by cancer cells. Transforming Growth Factor-β (TGFβ)-dependent signalling is attributed to promote EMT in advanced stages of breast cancer. A comprehensive regulatory map of TGFβ induced EMT was developed through an extensive literature survey. The network assembled comprises of 312 distinct species (proteins, genes, RNAs, complexes), and 426 reactions (state transitions, nuclear translocations, complex associations, and dissociations). The map was developed by following Systems Biology Graphical Notation (SBGN) using Cell Designer and made publicly available using MINERVA (http://35.174.227.105:8080/minerva/?id=Metastatic_Breast_Cancer_1). While the complete molecular mechanism of MBC is still not known, the map captures the elaborate signalling interplay of TGFβ induced EMT-promoting MBC. Subsequently, the disease map assembled was translated into a Boolean model utilising CaSQ and analysed using Cell Collective. Simulations of these have captured the known experimental outcomes of TGFβ induced EMT in MBC. Hub regulators of the assembled map were identified, and their transcriptome-based analysis confirmed their role in cancer metastasis. Elaborate analysis of this map may help in gaining additional insights into the development and progression of metastatic breast cancer.

O21 Raman spectroscopy for detection of squamous cell carcinoma in recessive dystrophic epidermolysis bullosa skin

Abstract Introduction and aims Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic skin disorder caused by biallelic pathogenic variants in COL7A1, which encodes type VII collagen (C7). Lack of C7 leads to blistering, chronic wounds, scarring and early onset of life-shortening squamous cell carcinomas (SCCs). Currently, the suspicion of SCC is mostly determined by clinical observation of visible changes in chronic wounds, and often requires multiple biopsies for histological diagnosis. This project aims to improve clinical care by developing a new noninvasive means of detecting SCC. To achieve this, we used Raman spectroscopy, a nondestructive analytical technique to study the changes occurring in RDEB skin when SCC is present, with the goal of creating a bedside test that can aid clinicians in the early diagnosis of SCC. Methods Raman spectroscopic imaging was performed on 7-µm frozen skin sections from RDEB (n = 3), RDEB SCC (n = 3) and normal skin (n = 3) to identify signalling changes between nonlesional and lesional states. An in-depth molecular composition analysis of the samples was performed using multivariate analysis with the goal of highlighting changes in abundance of specific molecules when SCC is present. Results For both nonmalignant and RDEB SCC skin sites we found specific Raman peaks associated with protein (1004 cm−1, 1650 cm−1) or lipids (1450 cm−1). RDEB SCC indicated a relative increase in DNA and protein. High-quality Raman spectroscopic images could be acquired that showed clear correlation with histological appearances. Current work is under way to determine which specific biological compounds contribute to the Raman spectra observed. Conclusions Raman spectroscopic imaging can provide comprehensive and noninvasive molecular tissue mapping with resolution comparable to histological sections, enabling molecular-based detection of SCC. Future work will focus on characterization of the SCC molecular profile, in addition to determining whether fibre optic Raman spectroscopy can be used to guide the biopsy/resection of RDEB lesions.

Spectroscopic characterization and quantum chemical calculations on Favipiravir-Guanine biomolecular complex

Favipiravir, a medication, has drawn a lot of interest recently as a possible therapeutic option for viral illnesses such as the COVID-19 pandemic. In the current work, Favipiravir + Guanine combination is being spectroscopically characterized using Fourier Transformed Infrared Spectroscopy, Raman, and Surface-Enhanced Raman Spectroscopy tools. Density functional theory along with the Becke 3-Parameter, Lee-Yang-Parr method and the basis set 6-311++ G(d,p) is used to explore the molecular interactions between the monomers of Guanine and Favipiravir. The stability of the complex resulting from the charge delocalization is thoroughly examined by natural bond orbital analysis that demonstrates the C=O∙∙∙H intermolecular hydrogen bond formation. The nature of the intermolecular hydrogen bond is described using atoms in molecules analysis. Molecular electrostatic potential mapping depicts various regions of electrostatic potential for the molecules, characterizing their reactive nature. The complex’s frontier molecular orbital gap of 2.39 eV indicates a higher possibility of electronic charge transfer, which in turn enhances the chemical reactivity of the complex. An analysis of the complex’s hyperpolarizability reveals a good non-linear optical response. The antiviral activity of the Favipiravir + Guanine complex is demonstrated by its molecular docking against the 6LU7 receptor (−5.61 kcal/mol).

Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.

Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.

Improved Mass Calibration in MALDI MSI Using Neural Network-Based Recalibration.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful imaging method for generating molecular maps of biological samples and has numerous applications in biomedical research. A key challenge in MALDI MSI is to reliably map observed mass peaks to theoretical masses, which can be difficult due to mass shifts that occur during the measurement process. In this paper, we propose MassShiftNet, a novel self-supervised learning framework for mass recalibration. We train a neural network on a data dependent and specifically augmented training data set to directly estimate and correct the mass shift in the observed spectra. In our evaluation, we show that this method is both able to reduce the absolute mass error and to increase the relative mass alignment between peptide MSI spectra acquired from FFPE-fixated tissue using a MALDI time-of-flight (TOF) instrument.

Exploring the spectral and nonlinear optical properties of phenyl isothiocyanate through density functional theory and molecular docking studies: A comprehensive analysis of a potent biologically active phytochemical

Quantum chemical calculations employing Density Functional Theory (DFT) with 6–31G (d,p) basis sets have yielded valuable insights into the molecular structure, Frontier Molecular Orbitals (FMOs), Mulliken Charges, and Molecular Electrostatic Potential Maps of the phenyl isothiocyanate (PITC) molecule. Spectral analysis of PITC has been conducted including Fourier transform infrared (FTIR), Fourier transform Raman (FT-RAMAN), Nuclear Magnetic Resonance (NMR), and ultraviolet–visible (UV–Vis) spectroscopy by theoretical method. Additionally, global descriptive parameters and thermal properties have also been determined. The Nonlinear Optical characteristic (NLO) has been assessed in the gas phase using the same level of theory. The investigation into toxicity revealed that the studied molecule exhibits drug-like characteristics and is non-toxic. Molecular docking studies have been employed to investigate hydrogen bond interactions, elucidating the minimal binding energy of the compound. The outcomes of the docking studies strongly suggest the significant biological activity of Phenyl Isothiocyanate, emphasizing its potential as a potent phytochemical.

Solvent Effects on the Absorption and Emission Spectra of the [5-amino-1-bromoindolizin-3-yl](4-bromophenyl)methanone Molecule.

The effects of solvent on the absorption and emission spectra and dipole moments of the 5ABBM have been extensively studied in a series of solvents. The dipole moments in the excited state are observed to be greater than those in the ground-state in all the solvents studied for the chosen molecule. The dipole moment increase in the excited singlet state ranges from 2.42 to 24.14 D. The experimentally calculated ground state and excited state dipole moments were determined using the solvatochromatic shifts in the absorption and emission spectra as a function of dielectric constant (ɛ) and refractive index (n). These data are used to estimate the excited-state dipole moment using the experimentally determined ground-state dipole moment. A series of fifteen different organic solvents (toluene, methanol, n-butyl alcohol, ethyl acetate, DMS, acetonitrile, benzene, isopropyl alcohol, water, DMF, DCM, DIO, THF, ethanol, and octanol) were investigated at constant dye concentrations. Small changes in the fluorescence spectrum were observed for the different solvents; the highest fluorescence intensity was observed for DMS, and the lowest was observed for water. The Stokes shift in different solvents was studied for the 5ABBM molecule. This results in molecule being more polar in the excited state than in the ground state for the solvents used. The ground state dipole moments, HOMO-LUMO, and molecular electrostatic potential maps were also computed via ab initio calculations and evaluated via Gaussian 09W software.

Identification of Rmg11 in tetraploid wheat as a new blast resistance gene with tolerance to high temperature.

Wheat blast caused by Pyricularia oryzae pathotype Triticum has spread to Asia (Bangladesh) and Africa (Zambia) from the endemic region of South America. Wheat varieties with durable resistance are needed, but very limited resistance resources are currently available. After screening tetraploid wheat accessions, we found an exceptional accession St19 (Triticum dicoccum, KU-114). Primary leaves of St19 were resistant not only to Brazilian isolate Br48 (a carrier of the type eI of AVR-Rmg8) but also to Br48ΔA8, an AVR-Rmg8 disruptant of Br48, even at 30℃, suggesting that the resistance of St19 is tolerant to high temperature and controlled by gene(s) other than Rmg8. When F2 population derived from a cross between St19 and St30 (a susceptible accession of T. paleocolchicum, KU-191) was inoculated with Br48, resistant and susceptible seedlings segregated in a 3:1 ratio, indicating that resistance of St19 is conferred by a single gene. We designated this gene as Rmg11. Molecular mapping revealed that the RMG11 locus is located on the short arm of chromosome 7A. Rmg11 is effective not only against other two Brazilian isolates (Br5 and Br116.5) but also against Bangladeshi isolates (T-108 and T-109) at the seedling stages. At the heading stages, lines containing Rmg11 were highly susceptible to the Bangladeshi isolates but moderately resistant to the Brazilian isolates. Stacking of Rmg11 with Rmg8 and the 2NS segment is highly recommended to achieve durable wheat blast resistance.

Evaluation of the binding efficacy of flavonol derivatives on estrogen receptors (ER) with respect to ring B hydroxylation

RationaleFlavonols are a class offlavonoidsthat have a 3-hydroxyflavonebackbone with an additional ketone group. Galangin is a form of flavonols formed with additional hydroxy groups at ring A positions 5 and 7. The hydroxylation at ring B of galangin may result in resonance and delocalization of electrons and the formation of different derivatives like kaempferol, quercetin, and myricetin. Most of these flavonols have a similarity to 17β-estradiol, the steroid sex hormone which bound to estrogen receptors (ER), a class of nuclear transcription factors involved in the regulation of many complex pathophysiological processes including breast cancer genesis and progression. Various studies have reported that most of the flavonols are antiestrogenic and show anticancer potential, but the mechanisms may be varied like estrogenic, anti-estrogenic, non-estrogenic, and biphasic activities and their mechanisms of action have not been systematically evaluated. AimThe goal of this study is to ascertain the possible interactions of flavonol derivatives to ER with respect to ring B hydroxylation and the unsaturation degree of the C2′=C3′ bond. MethodsThe variations in structure, frontier molecular orbital, molecular electrostatic potential maps, Mullikan charge population of derivatives was determined by Density functional theory (DFT) calculations at B3LYP/6-311G (d,p) level on model molecular systems. A deep insight into these interactions with ER was described by molecular docking studies. Results and discussionResults shows that the flavonol was found more affinity to ERβ and the efficacy was increased with respect to the OH group on ring B. The hydroxyl group at position 3 and 5 in ring A and C are not found much relevant. The site of ERβ is more hydrophilic while binding ligand and the electropositive and electronegative area of the molecule was increased and reaches a maximum for quercitin with the 3 OH group; after that, it found to diminish. Moreover, the reduced cavity size of ERβ and the replacement of LEU 384 with polar HIE 475 and MET 336 increased the polarity and hydrophilicity of the cavity and led to more electrostatic interaction with ligands. ERα is found to be hydrophobic and the polar interaction between the ligands and ERa is less due to open confirmation of the cavity and bulk empty space. The results also emphasize that myricetin and quercetin require less energy to activate while accounting for the values of Gibbs free energy, the electronic configuration of frontier molecular orbitals, and entropy. ConclusionThe hydroxylation on ring B has a significant importance in the chemical reactivity as well as estrogenic activity of flavonol.

GWAS advancements to investigate disease associations and biological mechanisms.

Genome-wide association studies (GWAS) have been instrumental in elucidating the genetic architecture of various traits and diseases. Despite the success of GWAS, inherent limitations such as identifying rare and ultra-rare variants, the potential for spurious associations, and in pinpointing causative agents can undermine diagnostic capabilities. This review provides an overview of GWAS and highlights recent advances in genetics that employ a range of methodologies, including Whole Genome Sequencing (WGS), Mendelian Randomization (MR), the Pangenome's high-quality T2T-CHM13 panel, and the Human BioMolecular Atlas Program (HuBMAP), as potential enablers of current and future GWAS research. State of the literature demonstrate the capabilities of these techniques in enhancing the statistical power of GWAS. WGS, with its comprehensive approach, captures the entire genome, surpassing the capabilities of the traditional GWAS technique focused on predefined Single Nucleotide Polymorphism (SNP) sites. The Pangenome's T2T-CHM13 panel, with its holistic approach, aids in the analysis of regions with high sequence identity, such as segmental duplications (SDs). Mendelian Randomization has advanced causative inference, improving clinical diagnostics and facilitating definitive conclusions. Furthermore, spatial biology techniques like HuBMAP, enable 3D molecular mapping of tissues at single-cell resolution, offering insights into pathology of complex traits. This study aims to elucidate and advocate for the increased application of these technologies, highlighting their potential to shape the future of GWAS research.

Thermal, X-ray spectroscopy, morphological, density functional theory and molecular modeling studies on yttrium(III), germanium(IV), tungsten(VI), and silicon penicillinate antibiotic complexes

This manuscript elucidates the thermal stability analysis of four distinct penicillinate complexes, comprising yttrium(III), germanium(IV), tungsten(VI), and silicon, over a temperature ranging from 25 to 800°C. Thermal data revealed the high thermal stability nature of the decomposition steps. According to the spectroscopic measurements, the chemical formula of penicillinate complexes were [Y(Pin)2].Cl.6H2O complex (1), [Ge(Pin)2].2Cl.2H2O complex (2), [W(Pin)2].4Cl complex (3), and [Si(Pin)2].2Cl.2H2O complex (4). The powder XRD pattern revealed crystalline to polycrystalline natures. The synthesized penicillinate complexes were subjected to theoretical calculations utilizing density functional theory (DFT) calculations, employing the lanL2DZ/6-311G++ level of theory. The optimized geometry of each penicillinate complex was discerned, and a comprehensive evaluation of various properties, including the HOMO→LUMO electronic energy gap, molecular electrostatic potential map, and additional physical parameters, was conducted and validated against experimental findings. Molecular docking tool was used to explore the anticancer activity of the synthesized penicillinate complexes in comparison with penicillin potassium drug (Pin). For the computational investigation, two kinases — CSF1R (PDB ID: 7MFC) and MEK2 (PDB ID: 1S9I) associated with breast cancer progression and estrogen-dependent breast cancer were utilized. This comprehensive analysis provides a deeper understanding of the synthesized penicillinate complexes and their potential applications. KEY WORDS: Penicillinate complexes, TGA-DrTGA, TEM, XRD, DFT/TD-DFT, Molecular docking Bull. Chem. Soc. Ethiop. 2024, 38(4), 973-988. DOI: https://dx.doi.org/10.4314/bcse.v38i4.13

Theoretical Study of Radical Scavenging Antioxidant Activity of Coumarin Derivatives in Licorice Using DFT

Nowdays, much research is focused on exploring antioxidant activity based on natural compounds. Licorice, a traditional natural product rich in antioxidant components, has been widely used in clinical medicine. However, there is a lack of theoretical studies on the active components in licorice. In this context, the antioxidant activity of several common active components of coumarin derivatives in licorice was investigated using a density flooding theory (DFT) approach. The free radical scavenging ability of the compounds was achieved by hydrogen atom transfer (HAT), sequential electron transfer proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET) mechanisms. The effect of solvent on antioxidant activity was also investigated. It was found that in the gas and benzene phases, the compounds studied preferred to undergo the HAT mechanism, while SPLET was favoured in polar solvents. In addition to the above mechanism, the HOMO and LUMO energies of the compounds as well as molecular descriptors and electrostatic potential maps were calculated and applied to predict the antioxidant activity of the compounds. The above studies allow a better understanding of the mechanism of free radical scavenging activity of coumarin derivatives from licorice.

Exploring the adsorption of five emerging pollutants on activated carbon: A theoretical approach

The identification and management of contaminants of emerging concern (CECs) in water systems is crucial for protecting public and environmental health. This paper reports a theoretical approach to studying the adsorption of five CECs: Atrazine (ATZ), Caffeine (CAF), Carbamazepine (CBZ), Sulfamethoxazole (SMX), and Ibuprofen (IBU) - onto Activated Carbon (AC). A set of computational methods, including electrostatic molecular potential maps, conceptual density functional theory, Fukui functions, thermodynamic analysis, and tight-binding molecular dynamics simulations, were employed to analyze the electronic/energetic interactions and mechanisms involved in the adsorption of CECs on AC. The theoretical methodology offered valuable predictions on reactivity sites, stability, and binding mechanisms. Results showed that adsorption primarily occurred through non-covalent interactions like π-π electron donor-acceptor interactions, van der Waals forces, and hydrophobic interactions. Thermodynamic properties suggested the adsorption process was spontaneous and exothermic. However, for the AC/SMX system, the Gibbs free energy reveals that adsorption may be unfavorably compared to the other study systems. Molecular dynamics simulations validated the kinetic stability in the following order CAF (0.13 Å)>CBZ (0.23 Å)>ATZ (0.75 Å)> IBU (1.28 Å)>SMX (1.54 Å). This exploratory theoretical study provides a deep understanding of the interactions between AC and five CECs, aiding in the rational design and optimization of AC-based treatment systems for environmental and industrial applications.

Msx genes delineate a novel molecular map of the developing cerebellar neuroepithelium.

In the early cerebellar primordium, there are two progenitor zones, the ventricular zone (VZ) residing atop the IVth ventricle and the rhombic lip (RL) at the lateral edges of the developing cerebellum. These zones give rise to the several cell types that form the GABAergic and glutamatergic populations of the adult cerebellum, respectively. Recently, an understanding of the molecular compartmentation of these zones has emerged. To add to this knowledge base, we report on the Msx genes, a family of three transcription factors, that are expressed downstream of Bone Morphogenetic Protein (BMP) signaling in these zones. Using fluorescent RNA in situ hybridization, we have characterized the Msx (Msh Homeobox) genes and demonstrated that their spatiotemporal pattern segregates specific regions within the progenitor zones. Msx1 and Msx2 are compartmentalized within the rhombic lip (RL), while Msx3 is localized within the ventricular zone (VZ). The relationship of the Msx genes with an early marker of the glutamatergic lineage, Atoh1, was examined in Atoh1-null mice and it was found that the expression of Msx genes persisted. Importantly, the spatial expression of Msx1 and Msx3 altered in response to the elimination of Atoh1. These results point to the Msx genes as novel early markers of cerebellar progenitor zones and more importantly to an updated view of the molecular parcellation of the RL with respect to the canonical marker of the RL, Atoh1.

The influence of catalyst structure on acidic strength of –SO3H groups for alkyl levulinate synthesis from biomass–derived feedstocks using sulfonic acid functionalized flexible MOF catalyst

A Brönsted acidic BUT−8(Cr)–SO3H metal–organic framework was used for the synthesis of ethyl levulinate from two different biomass–derived platform chemicals viz. furfuryl alcohol and levulinic acid. The catalyst was well characterized using various methods such as PXRD, FTIR spectroscopy, acid–base titration, NH3–TPD, TGA–DTA, SEM, TEM as well as the computational density functional theory (DFT) method. The performance of BUT–8(Cr)–SO3H catalysts was found to be superior to other catalysts (HZSM–5, H–Beta, and amberlyst –15) taken in this study. The sulfonic acid moieties bound to the aromatic naphthalene structure of BUT–8(Cr)–SO3H MOF were found to have a much stronger influence on the catalytic performance than the sulfonic acid moieties bound to the styrene framework of amberlyst–15. The key discoveries regarding the Brönsted acidic characteristics were computed via DFT incorporating the hydrogen removal energy, molecular electrostatic potential maps, and stability of the conjugate base of –SO3H moieties. The trend in the DFT–derived values was in the following order: BUT–8(Cr)–SO3H > Linker–naph –SO3H > Amberlyst–15. The results also indicate the influence of Cr metal on MOF structure to increase the acidic strength of the –SO3H group. The reaction optimization using DOE, recyclability, leaching study, and substrate scope study for both pathways using BUT–8(Cr)–SO3H were obtained.

Studies on Screening and Inheritance of Yellow Stem Borer (Scirpophaga incertulas Walker) Resistance in F2 and F3 Segregating Generations of Rice (Oryza sativa L.)

This study investigated the screening and inheritance of resistance to yellow stem borer (Scirpophaga incertulas) in F2 and F3 segregating generations of rice (Oryza sativa L.) derived from six crosses viz., ADT 43 X TKM 6, ADT 43 X ASD 12, ADT 45 X TKM 6, ADT 45 X ASD 12, ASD 16 X TKM 6 and ASD 16 X ASD 12. Field screening was conducted during the 2021 and 2022 kharif seasons, evaluating white ear damage as an indicator of resistance. The F2 and F3 populations showed a range of resistance levels from highly resistant to highly susceptible across the six crosses of rice. The distribution of resistance varied, with the cross ASD 16 x TKM 6 having the highest number of highly resistant plants in F2, while ADT 45 x ASD 12 had the lowest in both generations. Chi-square analysis revealed that the inheritance of resistance followed a complementary gene action epistasis with a 9-resistant to 7 susceptible ratios observed in all six crosses across both generations. The screening helped identify promising yellow stem borer resistant segregants, which can be further investigated at the genomic level for molecular characterization and mapping of resistance QTLs to facilitate their introgression into rice breeding programs.

Advancements of Breeding and Genomics in Wheat (Triticum aestivum L.): Enhancing Yield and Nutritional Value for Sustainable Agriculture

Advancements in wheat breeding and genomics presently explores the genomic interventions driving focusing on quantitative trait loci (QTL) mapping, marker-assisted selection (MAS) and genomic selection (GS). QTL mapping emerges as a pivotal method for pinpointing markers linked with desirable traits, facilitating MAS. Furthermore, genomic selection (GS) holds immense potential for crop improvement. It also delves into the current landscape of MAS and explores various prospects of GS for wheat biofortification. Looking ahead, accelerated mapping studies combined with MAS and GS schemes are poised to further enhance wheat breeding efficiency. Dense molecular maps and a large set of ESTs (Expressed Sequence Tags) have enabled genome-wide identification of gene-rich and gene-poor regions, as well as QTL, including eQTL (Expression quantitative trait loci). Additionally, markers associated with major economic traits have facilitated MAS programs in some countries and enabled map-based cloning of several genes/QTL. Resources for functional genomics, such as TILLING and RNA interference (RNAi), alongside emerging approaches like epigenetics and association mapping, are further enriching wheat genomics research. In this review, we initially present cutting-edge genome-editing technologies in crop plants, with a specific focus on wheat, addressing both functional genomics and genetic enhancement. We subsequently delineate the utilization of additional technologies, including GWAS, high-throughput genotyping and phenotyping, speed breeding, and synthetic biology, within the context of wheat breeding. We assert that integrating genome editing with other molecular breeding strategies will significantly expedite the genetic enhancement of wheat, thus contributing to sustainable global production.

Quantitative aspects of ToF-SIMS analysis of metals and alloys in a UHV, O2 and H2 atmosphere

Although secondary ion mass spectrometry (SIMS) is a versatile method used in the fields of surface analysis, depth profiling and elemental and molecular mapping, it also lacks quantification capabilities. The main reason for this is the matrix effect, which influences the ionization yield of secondary ions with respect to the substrate from which the analyzed compounds originate. There are several approaches to reduce the matrix effect, and gas flooding is one of the easiest methods to apply. In this work, we have investigated the possibilities of the ToF-SIMS method for the quantification of selected metals and alloys containing these metals in different ratios by reducing the matrix effect in the presence of different atmospheres. The measurements were performed in the ultra-high vacuum (UHV) environment, H2 and O2 atmospheres. H2 flooding shows the most significant improvements compared to the UHV analysis, while O2 is also promising but has some limitations. Improvements are most evident for the transition metals Ti, Cr, Fe, Co and Ni employed in our study, while the p-block elements such as Al and Si do not change so extensively. The deviations from the true atomic ratios of selected transition metals in different alloys reach a maximum of only 46 % when analyzed in the H2 atmosphere. In contrast, these values are 66 and 228 % for the O2 atmosphere and UHV environment, respectively. Our results suggest that gas adsorption and consequent formation of a new matrix on the surface, especially in the case of hydrogen, reduces the differences between the different chemical environments and electronic structures of the surface. In this way, the quantitative aspects of the SIMS method can be improved.

Gametocidal genes: from a discovery to the application in wheat breeding.

Some species of the genus Aegilops, a wild relative of wheat, carry chromosomes that after introducing to wheat exhibit preferential transmission to progeny. Their selective retention is a result of the abortion of gametes lacking them due to induced chromosomal aberrations. These chromosomes are termed Gametocidal (Gc) and, based on their effects, they are categorized into three types: mild, intense or severe, and very strong. Gc elements within the same homoeologous chromosome groups of Aegilops (II, III, or IV) demonstrate similar Gc action. This review explores the intriguing dynamics of Gc chromosomes and encompasses comprehensive insights into their source species, behavioral aspects, mode of action, interactions, suppressions, and practical applications of the Gc system in wheat breeding. By delving into these areas, this work aims to contribute to the development of novel plant genetic resources for wheat breeding. The insights provided herein shed light on the utilization of Gc chromosomes to produce chromosomal rearrangements in wheat and its wild relatives, thereby facilitating the generation of chromosome deletions, translocations, and telosomic lines. The Gc approach has significantly advanced various aspects of wheat genetics, including the introgression of novel genes and alleles, molecular markers and gene mapping, and the exploration of homoeologous relationships within Triticeae species. The mystery lies in why gametes possessing Gc genes maintain their normality while those lacking Gc genes suffer abnormalities, highlighting an unresolved research gap necessitating deeper investigation.

Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives

This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound 3 h, followed closely by 6 h, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. In vivo oral toxicity studies were conducted for the most active compound 3 h, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of 3 h, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.