Heterocytous cyanobacteria are among the most prolific source of bioactive secondary metabolites, including anabaenopeptins (APTs). A terrestrial filamentous Brasilonema sp. CT11 collected in Costa Rica bamboo forest, as black mat was studied using a multidisciplinary approach: genome mining and HPLC-HRMS/MS coupled with bionformatic analyses. Herein, we report the nearly complete genome consisting 8.79 Mbp with a GC content of 42.4%. Moreover, we report on three novel tryptophane-containing APTs; anabaenopeptin 788 (1), anabaenopeptin 802 (2) and anabaenopeptin 816 (3). Further, the structure of two homologues, i.e., anabaenopeptin 802 (2a) and anabaenopeptin 802 (2b) was determined by spectroscopic analysis (NMR and MS). Both compounds were shown to exert weak to moderate antiproliferative activity against HeLa cell lines. This study also provides the unique and diverse potential of biosynthetic gene clusters and an assessment of the predicted chemical space yet to be discovered from this genus.

Various studies indicate that vaccination, especially with pneumococcal vaccines, protects against symptomatic cases of SARS-CoV-2 infection and death. This paper explores the possibility that pneumococcal vaccines in particular, but perhaps other vaccines as well, contain antigens that might be cross-reactive with SARS-CoV-2 antigens. Comparison of the glycosylation structures of SARS-CoV-2 with the polysaccharide structures of pneumococcal vaccines yielded no obvious similarities. However, while pneumococcal vaccines are primarily composed of capsular polysaccharides, some are conjugated to CRM197, a modified diphtheria toxin, and all contain about three percent protein contaminants, including the pneumococcal surface proteins PsaA, PspA and probably PspC. All of these proteins have very high degrees of similarity, using very stringent criteria, with several SARS-CoV-2 proteins including the spike protein, membrane protein and replicase 1a. CRM197 is also present in Hib and meningitis vaccines. Equivalent similarities were found at lower rates, or were completely absent, among the proteins in diphtheria, tetanus, pertussis, measles, mumps, rubella, and poliovirus vaccines. Notably, PspA and PspC are highly antigenic and new pneumococcal vaccines based on them are currently in human clinical trials so that their effectiveness against SARS-CoV-2 disease is easily testable.

COVID-19 is a novel severe acute respiratory syndrome coronavirus. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CL^pro) bound to a synthetic inhibitor which represents a major druggable target. The druggability of Mpro could be used for discovering drugs to treat coronavirus disease 2019. It was carried out a multi-level computational study to evaluate the potential anti-viral properties of the components of the medicinal herb Uncaria tomentosa (Cat´s claw) focusing on the inhibition of M^pro. The in-silico approach starts with protein-ligand docking of 26 Cat’s claw key components followed by ligand pathway calculations, molecular dynamics simulations and MM-GBSA calculation of the free energy of binding for the best docked candidates. The structural bioinformatics approaches led to the identification of three bioactive compounds of Uncaria tomentosa (Speciophylline, Cadambine and Proanthocyanidin B2) with potential therapeutic effects by strong interaction with 3CLpro. Additionally, in silico drug-likeness indices for these components were calculated and show good predicted therapeutic profiles of these phytochemicals. Our findings suggest the potential effectiveness of Cat's claw as complementary and/or alternative medicine for COVID-19 treatment.

The outbreak across the globe due to coronavirus disease 2019 (COVID-19) has spread abruptly by infected humans worldwide. The continuous efforts by scientists is on way to understand how pandemic of COVID-19 resembles and differs from serve acute respiratory syndrome coronavirus (SARS-CoV) at transcriptomic and genomic level. The SARS-CoV and COVID-19 exploits the angiotensin converting enzyme 2 (ACE2) receptor to gain entry inside the cells.We analyzed the entry COVID-19 into host cell due to receptor binding domain (RBD) of spike glycoprotein. The proposed simulation data shows similar ternary structures from two viruses shares approximately 80 percent identity in amino acid sequences. Our molecular modeling investigation signifies that angiotensin converting enzyme 2 (ACE2) has stronger interaction with COVID -19 RBD. The Amino acid phenylaniline F486 LOOP plays vital role due to its penetration into hydrophobic pocket in ACE2.The said investigation of S-Glycoprotein RBD of COVID-19 or SARS-CoV-2 via ACE2 provides post genome analysis of protein-protein interaction for rapid assessing transmission of infected patients by deadly CoVID-19. The scientific data extracted implies early guidance to control and viral prevention of CoVID-19.

Coronavirus disease 2019 (COVID-19) was recently appeared all over the world. The viral main protease (3-chymotrypsin-like cysteine enzyme) controls COVID-19 duplication and manages its life cycle, making it a drug discovery target. Therefore, herein, we analyzed the theoretical approaches of 10 structurally different hydrolysable tannins as natural anti-COVID-19 through binding with the main protease of 2019-nCoV using molecular docking modelling via Molecular Operating Environment (MOE v2009) software. Our results revealed that there are top three hits may serve as potential anti-COVID-19 lead molecules for further optimization and drug development to control COVID-19. Pedunculagin, tercatain, and punicalin were found to faithfully interact with the receptor binding site and catalytic dyad (Cys145 and His41) of COVID-19 main protease, showing their successfully inhibit the protease enzyme of 2019-nCoV. We anticipated that this study would pave way for tannins based novel small molecules as more efficacious and selective anti-COVID-19 therapeutic compounds.

The molecular dynamics simulation has been used to investigate the structural and transport properties of (Ba_0.5-xSr_x)La_0.5InO_3-δ (x=0, 0.1, 0.2) oxygen-ion conductor. The previous studies reported that the ionic conductivity of Ba-doped LaInO3 decreases because Ba dopant forms narrow oxygen path in the lattice, which could hinder the diffusion of oxygen ion. In this study, we reveal the mechanism to improve the ionic conductivity by Ba and Sr co-doping on La site in LaInO3 perovskite oxide. The results show that the ionic conductivity of (Ba_0.5-xSr_x)La_0.5InO_3-δ increases with increasing numbers of Sr ions, which oxygen diffusion paths including Sr ion have larger critical radius than Ba ions. The RDF calculations showed the heights of peak in composition including Sr ions is lower and broaden, so oxygen ions moved easily into other oxygen sites.

Pulse oximetry is the current standard for detecting drops in arterial blood oxygen saturation (SpO₂) associated with obstructive sleep apnea and hypopnea events in polysomnographic (PSG) testing. In cases of hypoxic challenge, such as occurs during apneic events, regulatory mechanisms restrict blood flow to the skin to preferentially maintain SpO₂ for more vital organs. As a result, a measure related to skin tissue oxygenation is likely to be more sensitive to inadequate breathing during sleep than pulse oximetry. Energy Conversion Monitoring (ECM) provides a method for measuring skin tissue oxygen-dependent energy conversion and, as such, is promising for more sensitively detecting sleep disordered breathing (SDB) events compared to pulse oximetry. We hypothesized that ECM would detect hypoxia occurring with SDB events associated with drops in SpO₂ but also would detect hypoxic challenge occurring with SDB events not associated with drops in SpO₂ (hypopneas defined by a drop in nasal pressure occurring in conjunction with an arousal, respiratory-related arousals, and primary snoring). Primary snoring is of particular interest with respect to the potential of ECM because it is statistically associated with co-morbidities of SDB, such as hypertension, but is not considered pathological because of the lack of a proximal measure of pathology occurring with PSG. In this article we review ECM technology and methodology, present preliminary data indicating that it detects hypoxia occurring in the skin during SDB events that is not detected as blood desaturation by pulse oximetry, and make the case that it is a promising tool for identifying pathology occurring at the mild end of the SDB spectrum.

This work examines atomic and molecular signatures in laser-induced plasma in standard ambient temperature and pressure environments, including background contributions to the spectra that depend on the laser pulse-width. Investigations include solids, gases, and nano-particles. Abel inversions of measured line-of-sight data reveal insight into the radial plasma distribution. For nominal 6 nanosecond laser pulses and for pulse-energies in the range of 100 to 800 mJ, expansion dynamics and turbulence due to shock phenomena are elucidated to address local equilibrium details that are frequently assumed in spatially averaged emission spectroscopy. Chemical equilibrium computations reveal temperature dependence of selected plasma species. Specific interests include atomic hydrogen (H) and cyanide (CN). Atomic hydrogen spectra indicate axisymmetric shell structures and isentropic expansion of the plasma kernel over and above the usual shockwave. The recombination radiation of CN emanates within the first 100 nanoseconds for laser-induced breakdown in a 1:1 CO2:N2 gas mixture when using nanosecond laser pulses to create the micro-plasma. The micro-plasma is generated using 1064 nm, 150 mJ, 6 ns Q-switched Nd:YAG laser radiation. Measurements of the optical emission spectra utilize a 0.64 m Czerny-Turner type spectrometer and an intensified charge-coupled device.

An autonomous endogenous time-keeping is ubiquitous across many living organisms known as circadian clock when it has a period of about 24 hours. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus \textit{Neurospora crassa} is a well established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of \textit{Neurospora} is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedbacks among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 hrs. Our model reveals a switch between WC1 induced transcription and FFC assisted inactivation of WC1. Using the new model we also study possible mechanisms of glucose compensation. A fairly simple model with just 3 non-linearities helps to elucidate clock dynamics revealing a mechanism of rhythms production. The model can further be utilized to study entrainment and temperature compensation.

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite the significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialog between legumes and rhizobia, if so, what part of the molecular dialog is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, genes controlling the nodulation process, were significantly reduced in Pi-deficient common bean seedlings. Further transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Additionally, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule number, was higher in Pi-deficient seedlings than in control seedlings. The data presented in this study shed light on the understanding of how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia.

The search for graphene or few layer graphene production methods that are simple, allow mass production and yield good quality material continues to provoke intense investigation. The present work contributes through the study of the aqueous exfoliation of four types of graphene sources, namely graphite and graphite nanoflakes with different morphologies and geographical origin. The exfoliation was achieved in an aqueous solution of a soluble pyrene derivative that was synthesized to achieve maximum interaction with the graphene surface at low concentration (5 x 10-5 M). The yield of bilayer and few layer graphene obtained was quantified by Raman spectroscopic analysis and the adsorption of the pyrene derivative on the graphene surface was studied by thermogravimetric analysis and X-ray diffraction. The whole procedure was rationalized with the help of molecular modeling.

Based on a new model of a possible origin of life, we establish an efficient and stable system undergoing structural reproduction, self-optimization and molecular evolution. This system is being formed under realistic conditions by the interaction of two cyclic processes, one of which offering vesicles as the structural environment, the other supplying peptides from a variety of amino acids as versatile building blocks. We demonstrate that structures growing in a combination of both cycles have the potential to support their own existence, to undergo chemical and structural evolution and to develop unpredicted functional properties. The key mechanism is the mutual stabilization of the peptides by the vesicles and of the vesicles by the peptides together with a constant production and selection of both. The development of the proposed system over time not only would represent one of the principles of life, but could also be a model for the formation of self-evolving structures ultimately leading to the first living cell. The experiment yields clear evidence on a vesicle-induced accumulation of membrane-interacting peptide which could be identified by liquid chromatography combined with high-resolution mass spectroscopy. We found that the selected peptide has an immediate effect on the vesicles, leading to i) reduced vesicle size, ii) increased vesicle membrane permeability, and iii) improved thermal vesicle stability.

The emission of [O I] lines in the coma of Comet 67P/Churyumov-Gerasimenko during the Rosetta mission have been explained by electron impact dissociation of water rather than the process of photodissociation. This is the direct evidence for the role of electron induced processing has been seen on such a body. Analysis of other emission features is handicapped by a lack of detailed knowledge of electron impact cross sections which highlights the need for a broad range of electron scattering data from the molecular systems detected on the comet. In this paper we present an overview of the needs for electron scattering data relevant for the understanding of observations in coma, the tenuous atmosphere and on the surface of 67P/Churyumov-Gerasimenko during the Rosetta mission. The relevant observations for elucidating the role of electrons come from optical spectra, particle analysis using the ion and electron sensors and mass spectrometry measurements. To model these processes electron impact data should be collated and reviewed in an electron scattering database and an example is given in the BEAMD, which is a part of a larger consortium of Virtual Atomic and Molecular Data Centre – VAMDC.

A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds like nucleobases, sugars or peptides principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments, the latter offering preferential starting conditions for a subsequent RNA world.

Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques are readily used by ecologists to visualize and explain differences between study sites, they could theoretically be employed to differentiate organisms within an experimental framework while simultaneously identifying response variables that drive documented experimental differences. Therefore, MSA were used herein to attempt to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes using data from laboratory-based temperature challenge studies performed in Southern Taiwan. Gene expression and physiological data partitioned experimental specimens by time of sampling, treatment temperature, and site of origin upon employing MSA, signifying that S. hystrix and its dinoflagellate endosymbionts display physiological and molecular signatures that are characteristic of sampling time, site of colony origin, and/or temperature regime. These findings promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change.

COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, TMPRSS2, and AP2-associated protein kinase 1. In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of drug candidates to target receptors, providing insight into their potential efficacy. However, it is crucial to consider both the advantages and limitations of these studies and to complement them with experimental validation to ensure the efficacy and safety of identified drug candidates.

This article discusses laser-induced laboratory-air plasma measurements and analysis of hydroxyl (OH) ultraviolet spectra. New experiments with Q-switched laser pulses illustrate occurrence of molecular recombination spectra for time delays of the order of several dozen of microseconds after plasma initiation. The computation of the emission spectra utilizes line strength data that are communicated as a supplementary file. Applications of detailed OH computations include laser-induced plasma and combustion analyses, to name but two applications.

The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which combined hydrogen-deuterium exchange (HDX), quantitative protein-protein and protein-nucleic acid cross-linking (XL), and homology analysis, to model the structure of the complex between the full-length DNA binding domain (DBD) of FOXO4 and its DNA binding element (DBE). The results confirmed that FOXO4-DBD assumes the characteristic forkhead topology shared by these types of transcription factors, but its binding mode differs significantly from those of other members of the family. The results showed that the binding interaction stabilized regions that were rather flexible and disordered in the unbound form. Surprisingly, the conformational effects were not limited only to the interface between bound components but extended also to distal regions that may be essential to recruiting additional factors to the transcription machinery. In addition to providing valuable new insights into the binding mechanism, this project provided an excellent evaluation of the merits of structural proteomics approaches in the investigation of systems that arematerial not directly amenable to traditional high-resolution techniques.

Gliomas are common primary central nervous system (CNS) tumours which are often very difficult to diagnose, stage and manage because of their heterogeneity and molecular aberrations. The notable hallmark of gliomas is integrated genome mutations and methylome that correlates with distinctive patterns of transcription that potentiates glioma heterogeneity, angiogenesis and ultimately poor prognosis. The World Health Organization (WHO) has decided to reclassify gliomas based on molecular markers rather than the traditional anatomical basis; use of Nuclear Medicine techniques e.g. SPECT/PET and Magnetic Resonance Imaging (MRI) techniques based on molecular markers is set to become the future gold standards. This has led to the investigations on potential for the use of non-invasive imaging techniques such as [68Ga]68Ga-RGD positron emission tomography (PET) to be utilised routinely in clinical practice based on angiogenic markers and also the potential to add information that may assist in drug-design and therapeutic decision making. This review aims to provide an overview of the basis of recent advances in glioma imaging using molecular targeting with positron emission tomography and SPECT imaging, as well as the role in patient management i.e. diagnosis, staging, recurrence detection etc.

The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR-type 2 angiogenesis and vascular morphogenesis as the tyrosin kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in both stimulating and inhibitory ways. This investigation aims to examine the molecular properties of VEGFR2, a molecule primarily involved in the processes of vasculogenesis and angiogenesis. These relationships were defined by the interactions between vascular endothelial growth factor receptor 2 (VEGFR2) and the structural features of the systems. The chemical space of the inhibitory peptides and stimulators was described using topological and energetic properties. Furthermore, chimeric models of stimulating and inhibitory proteins (for VEGFR2) were computed using the protein system structures. The interaction between the chimeric proteins and VEGFR was computed. The chemical space was further characterized using complex manifolds and high-dimensional data visualization. The results show that a slightly similar chemical area is shared by VEGFR2 and is shared by stimulating and inhibitory proteins. On the other hand, the stimulator peptides and the inhibitors have distinct chemical spaces.

The aim of this study was to investigate the relationship between postprandial glycemic levels based on flash-monitoring and the production of intestinal hydrogen (H2) and methane (CH4) gases based on measurement of the amount of these gases in exhaled air. We studied 14 subjects with type 2 diabetes mellitus (T2DM) and 10 individuals without diabetes (control) with 3 food-load tests with simultaneous determination of gases in exhaled air and assessment of glucose levels. In 15.4% of patients with T2DM, there was a non-significant increase in exhaled H2. How-ever, all subjects in the control group had significant increase in exhaled H2. Moreover, the level of H2 in exhaled breathafter food load in patients with T2DM was lower than in normoglycemic subjects. Also, in normoglycemic subjects there was an inverse correlation between maximum glucose rise and maximum H2 in exhaled air after food load. At the same time in patients with T2DM the level of CH4 in exhaled air directly correlated with the parameters of postprandial glycemia in the test with lactulose. Confirmation of a causal relationship between decreased H2 production, increased intestinal CH4 production, and more severe postprandial glycemia may identify new therapeutic targets in the correction of postprandial glycemia in patients with T2DM.

This study presents a detailed computational investigation aimed at identifying and evaluating potential small organic molecular scaffolds as inhibitors targeting the Pks13 protein, a critical enzyme in tuberculosis (TB) drug discovery. Our approach integrates multiple computational techniques, including quantitative structure-activity relationship (QSAR) modelling, compound library generation, molecular docking, biological activity prediction, re-evaluation of screened compounds, molecular dynamics (MD) analysis, and binding free energy estimation using the MM-GBSA approach. We developed a robust QSAR model using multiple linear regression (MLR) techniques, specifically tailored to predict the minimum inhibitory concentration (MIC) values of potential anti-TB agents. This model demonstrated excellent predictive performance, validated through rigorous internal and external validation procedures. Through molecular docking simulations, we identified five promising inhibitors Ethyl (R,Z)-2-(2-((2-chlorobenzyl) oxy)benzylidene)-5-(4-chlorophenyl)-7-methyl-3-oxo-2,3-dihydro-5H-thiazolo [3,2-a] pyrimidine-6-carboxylate (PKD1), (7R,9aR)-7-(2-hydroxyphenyl)-4-(2-methoxyphenyl)-3-methyl-7,8,9,9a-tetrahydroisoxazolo[5,4-b]quinolin-5(6H)-one (PKD2), (7-(4-methoxy phenyl)-2-methyl-3-phenylpyrazolo[1,5-a]pyrimidin-5-yl)(4-(3-(trifluoromethyl)phenyl) piperazin-1-yl)methanone (PKD3), (8S,10S)-10-(((2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl tetrahydro-2H-pyran-2-yl)oxy)-6,8,11-trihydroxy-8-(2-hydroxyacetyl)-1-methoxy-7,8,9,10-tetra-hydrotetracene-5,12-dione (PKD4), 3-(3,4-dimethylphenyl)-5-((2-(4-fluorophenyl)-2-oxoethyl) thio)-6-phenyl-2-thioxo-2,3,5,7a-tetrahydrothiazolo[4,5-d]pyrimidin-7(6H)-one (PKD5)with high binding affinities, prioritizing them based on their binding energies. These selected compounds were further assessed for their biological activity predictions, guiding the selection of candidates for experimental validation. Subsequent re-evaluation using absolute binding free energy estimation and MD simulations provided insights into the stability and dynamics of the protein-ligand complexes over time. Our findings highlighted the potential of identified compounds as stable binders within the Pks13-TE domain binding pocket, underscoring their viability as drug candidates. Additionally, binding free energy analysis using MM-GBSA reaffirmed the strong affinity of the proposed compounds towards Pks13. Our integrated computational approach offers a systematic and detailed framework for the identification and characterization of potential Pks13 inhibitors with specific relevance to TB drug discovery.

Developing clinically meaningful nanomedicines for cancer therapy requires the drugs to be effective, safe, simple, cheap, and easy to store. In the present work, we report that a simple cationic Fe(III)-rich salt of [FeIIICl(TMPPH2)][FeIIICl4]2 (Fe-TMPP) exhibits a superior anticancer performance toward a broad spectrum of cancer cell lines, including breast, colorectal cancer, liver, pancreatic, prostate, and gastric cancers, with half maximal inhibitory concentration (IC50) values in the range of 0.098−3.97 μM (0.066−2.68 μg mL−1), and comparable to the best-reported medicines. Fe-TMPP can forms stand-alone nanoparticles in water without the need for extra surface modification or organic-solvent-assisted antisolvent precipitation. Critically, Fe-TMPP is TME-responsive (TME = tumor microenvironment), and can only elicit its function in the TME with overexpressed H2O2, converting H2O2 to the cytotoxic •OH to oxidize the phospholipid of the cancer cell membrane, causing ferroptosis, a programmed cell death process of cancer cells.

Hyperuricemia is mainly caused by the overproduction of uric acid (UA) catalyzed from xanthine by xanthine oxidase (XO) in abnormal purine metabolism in human body. There is an increasing demand for developing novel XO inhibitors of plant origins. The inhibition kinetics and type as well as actions of hesperetin against XO were investigated in vitro using multi-spectroscopic methods including UV-Vis absorption, Fourier transform infrared spectroscopy (FT-IR), fluorescence spectroscopy and molecular docking simulation. Results indicated that hesperetin reversibly inhibited XO in a competitive manner with an inhibition constant (Ki) value of (2.15 ± 0.05) × 10-6 mol/L. Hesperetin had a higher scavenging rate against O2- radical generated by the XO reaction system. The binding of hesperetin to the active site of XO altered the protein’s secondary structure as demonstrated by FT-IR and fluorescence spectra. Molecular docking study revealed that hesperetin had highly affinity to XO and the bonding of hesperetin to the molybdopterin (Mo-pt) active center inhibited not only substrate entry, but also prevented oxygen binding to flavin adenine dinucleotide (another active center in XO). Additionally, hydrophobic interactions and hydrogen bonds contributed to the stabilization of the hesperetin-XO complex. The results suggested that hesperetin be a promising natural XO inhibitor to alleviate hyperuricemia and gout.

Accurate clinical diagnosis of patients presenting to primary care settings with acute sore throat remains challenging, often resulting in the over-prescribing of antibiotics. Using point-of-care tests (POCTs) to differentiate between respiratory infections is well-accepted, yet evidence on the application within primary care is sparse. We assessed the application of testing patients (n=160) from three family practices with suspected Streptococcal infections using rapid molecular tests (ID NOW Strep A2, Abbott). In addition to comparing clinical evaluation and prescription rates with either usual care or with testing, patients and staff completed a questionnaire about their experience of molecular POCT in primary care. The immediate availability of the result was important to patients (100%) and staff (≈90%) stated that molecular testing improved quality of care. Interestingly, only 22.73% of patients with a Centor score >2 tested positive for Strep A and overall, less than 50% of Centor scores 3 and 4 tested positive for Strep A with the ID NOW testing platform. The addition of rapid molecular POCTs to clinical assessment resulted in a 55- 65% reduction in immediate and deferred antibiotic prescriptions. The intervention was popular with patients and medical staff but was associated with increased cost and a longer appointment length.

Coarse-grained molecular dynamics simulations are employed to investigate the spatiotemporal evolution of vesicles (polymersomes) by the self-assembly of randomly distributed amphiphilic BAB triblock copolymers with hydrophilic A and hydrophobic B blocks in an aqueous solution. The vesiculation pathway consists of several intermediate structures, such as an interconnected network of copolymer aggregates, a cage of cylindrical micelles and a lamellar cage. The cage-to-vesicle transition occurs at a constant aggregation number and practically eliminates the hydrophobic interfacial area between the B block and solvent. Molecular reorganization under-lying the sequence of morphology transitions from a cage-like aggregate to a vesicle is nearly isentropic. The end-to-end distances of isolated copolymer chains in solution and those within a vesicular assembly follow log normal probability distributions. This is attributed to the pre-ponderance of folded chain configurations in which the two hydrophobic end groups of a given chain stay close to each other. However, the probability distribution of end-to-end distances is broader for chains within the vesicle as compared to that of a single chain. This is due to the swelling of the folded configurations within the hydrophobic bilayer. Increasing the hydropho-bicity of the B block reduces the vesiculation time without qualitatively altering the self-assembly pathway.

The main inhibitory neurotransmitter in the mammalian brain is 4-aminobutyric acid (GABA). Phthalimide acts as a sodium channel antagonist, one of the finest targets for treating epilepsy is the sodium channel and JNK kinase activity is inhibited to treat epilepsy. a novel compound with multiple targets of action for the treatment of epilepsy also anti-oxidant activity has been designed. The compounds are designed in two series aldehydes and aniline. Docking of all the designed compounds has been done with the suitable protein GABA-AT, sodium channel, JNK protein, and anti-oxidant from protein bank. QSAR was done for constructing many linear regression models. In combination with the developed Docking and QSAR outcomes, ADMET has been performed for the active compounds. The result shows that 11 of the compounds have excellent binding energy in docking with all the receptors and also have good QSAR results and follow the ADMET. The structural understanding of human GABA-AT inhibition was obtained from molecular dynamics simulation studies for compound no. 11 at 5 nanoseconds. Synthesis and pharmacological activity also suggest that the designed compound no.11 be considered the best Novel Compound.

Helical (frontier) molecular orbitals [Chem. Sci. 2013, 4, 4278] have been reported almost a decade ago. Yet, helical molecular spin densities [Mol. Phys. 2022, e2157774] have been observed by us only very recently. In this work, we have observed that some chiral boron clusters (B–16, B–20, B–24, and B–28) can simultaneously have helical molecular orbitals and helical spin densities. To our best knowledge, it is the first time we have discovered that inorganic boron clusters assume such an unprecedented property. We have unambiguously unraveled that it is chiral Jahn-Teller distortion of quasi-planar boron clusters that drives the formation of helical molecular spin densities. More interestingly, we have shown that elongation/enhancement of helical molecular orbitals can be achieved by simply adding more building blocks via a linker. Aromaticity properties of these boron clusters are also discussed. Implication of this work is straightforward that boron clusters may find potential applications in spintronics, such as molecular magnets.

Environmental DNA (eDNA) sampling has emerged as a powerful approach for monitoring biodiversity in the context of diverse terrestrial and aquatic ecosystems, and has broad potential for both environmental surveys and species management. eDNA studies focusing on plant and animal species have capitalized on analytical methodologies developed originally for metagenomic studies of microorganisms, and on technological improvements in sample collection. However, while eDNA studies have proliferated rapidly, efforts to standardize sampling and analytical methods are still nascent. Critically, fundamental data concerning the distribution and persistence of eDNA in different ecological contexts are lacking, complicating both confidence in species detection and comparability between studies. We propose that key deficits could be addressed by using well-designed synthetic DNA standards or tracers, which are widely used in fields ranging from medical diagnostics to hydrology. In-field application of a standardized mixture of barcoded synthetic DNA fragments of varying lengths and concentrations that are recovered concommitantly with eDNA sampling should provide critical yet missing data on environmental DNA distribution and turnover, as well as an internal molecular standard to enhance both species detection and comparability between eDNA studies.

Explosive boiling is a fast phase transition from an ultra-thin liquid film to vapor under an extremely high heat flux, which typically has been studied using molecular dynamics simulation (MDS) method. The present MDS study investigated the explosive boiling of a liquid argon nanofilm over different solid copper surfaces with different nanowall patterns including parallel and cross nanowalls. For each surface, atomic motion trajectories, number of liquid and vapor argon atoms, heat flux, and, mainly, onset time of explosive boiling were investigated. The simulation results indicated that explosive boiling occurs earlier on parallel and cross nanowall surfaces than on an ideally smooth surface, regardless of the topology and configuration of nanowalls. Moreover, the results revealed that by using the cross nanowall surfaces, the onset time of explosive boiling decreased by 0.7–4% compared to the parallel nanowall surfaces. In addition, it was found that the onset time of explosive boiling strongly depends on the potential energy barrier and the movement space between nanowalls for both parallel and cross nanowall surfaces. Furthermore, simulation findings showed that even though increasing the height of cross nanowalls increases heat flux and temperature of the fluid argon domain, it does not necessarily result in a shorter onset time of explosive boiling. These findings demonstrate the capability of cross nanowall surfaces for explosive boiling, thereby could be utilized in future surface design for thermal management applications.

Background: The efficacy of local therapies for lung cancer patients with postoperative oligo-recurrence has been reported. However, whether local therapies should be chosen over molecular targeted therapies for oligo-recurrence patients with driver mutations remains controversial. We hence aimed to investigate the optimal initial treatment strategy for oligo-recurrence in lung cancer patients with driver mutations. Methods: Among 2,152 patients with lung adenocarcinoma who underwent surgical resection at our institute between 2008 and 2020, 66 patients with driver mutations who experienced cancer oligo-recurrence after surgery, and were treated with local or molecularly targeted therapy as an initial therapy after recurrence were evaluated. Oligo-recurrence was characterized by the presence of 1 to 3 recurrent lesions. These patients were investigated focusing on their post-recurrence therapies and prognoses. Results: The median follow-up period was 71 months. Local and molecular targeted therapies were administered to 41 and 25 patients, respectively. The number of recurrence lesions tended to be lower in the initial local therapy group than in the molecular targeted therapy group. In the initial local therapy group, 23 patients (56%) subsequently received molecular targeted therapies. The time from recurrence to the initiation of molecular targeted therapy was significantly longer in the local therapy group than in the molecular targeted therapy group (p < 0.001). There was no significant difference in post-recurrence overall survival (hazard ratio, 1.429; 95% confidence interval, 0.701–2.912; log-rank, p = 0.324), and post-recurrence progression-free survival (hazard ratio, 0.799; 95% confidence interval, 0.459–1.390; log-rank, p = 0.426) in the initial local ablative therapy group compared with the initial molecular targeted therapy group. Conclusions: Local therapies as a first-line treatment did not show statistically significant differences in post-recurrence survival or progression-free survival compared with molecular targeted therapies. However, local therapies as an initial treatment should be considered preferably, as it can cure the recurrence and can delay the start of administration of molecular-targeted therapies.

The study aims to evaluate the Quorum Sensing (QS) system inhibition against some Gram-positive and Gram-negative bacteria detected by molecular modeling of R. cathartica L. plant extract. R. cathartica L. methanol extract was evaluated in vitro. The research was carried out for the possible role and mechanism of R. cathartica L. The antibacterial activity of R. cathartica L. seed extract on some Gram-positive and Gram-negative strains was evaluated using culture-based and computational analysis. Gentamicin (CN; 30 µg/ml, Bioanalyse) was used as an antibacterial control of the extract on the production potential of QS-dependent virulence factors on Pseudomonas aeruginosa PAO1 was investigated. Phytochemical analysis resulted in the identification of 23 phenolic phytochemicals. R. cathartica L. extract was observed to have antimicrobial activity against Gram-positive and Gram-negative bacteria at different rates (11.3 mm-16 mm). The inhibitory effect of R. cathartica L. extract on P. aeruginosa PAO1 (elastase 61%, pyocyanin 18%, and biofilm 61%) was recorded moderately. Phytochemical analysis revealed that the main component of the extract is kaempferol. Therefore, the binding potential of kaempferol on QS system receptors was investigated via molecular docking. Computational analysis showed that kaempferol can inhibit the QS system by preventing competitive ligands from connecting to LasR. This study explored the activity and mechanism of action for a new green alternative against resistance. might provide a mechanism for R. cathartica L. seed extract components and thus provide a new avenue for using R. cathartica L. seed extract as a green antibacterial agent.

Chicken collagen is a promising raw material source to produce gelatins and hydrolysates. Gelatins and hydrolysates can be prepared biotechnologically using proteolytic enzymes produced by submerged fermentation of genetically modified microorganisms. By choosing the appropriate process conditions, such changes can be achieved at the molecular level of collagen, making it possible to prepare products with targeted properties for advanced cosmetic, pharmaceutical, medical or food applications. The research aims to investigate: i) antioxidant activity (DPPH and ABTS) in model samples of chicken collagen products (gelatin and hydrolysates); ii) distribution of molecular weights by the GPC-RID analysis method; iii) functional groups and configuration of polypeptide chains related to molecular level properties using FTIR; iv) the microbiological properties on SDA, PCA, TSA and VRBL microbial populations using MALDI method. Antioxidant activity towards ABTS radicals of more than 80% was found for all samples. The molecular weights of all gelatin samples showed typical α- and β-chains. FTIR analysis confirmed that the samples showed all typical vibrational regions for collagen cleavage products, Amide A and B, Amide I, II, and III at characteristic values. Microbiological analysis of the prepared samples showed no undesirable bacteria that would limit advanced applications of the prepared products. Gelatins and hydrolysates from chicken stomachs represent a promising alternative to products made from standard collagen tissues of terrestrial animals.

Molecular dynamics (MD) simulations present a sophisticated nano-scale computational approach that can play a critical role in material design for next generation batteries. One critical piece of information needed for MD simulations is the non-bonded potential parameters, which can be obtained through quantum mechanics (QM) calculations or experimental methods. However, experimental data is not available for exploratory and novel materials to derive the potential parameters. Also, the QM approach needs significant computational power and is too time consuming for large systems. On the other hand, current Artificial Intelligence techniques are faster, but they cannot be generalized across molecules and properties. As a result, there is a significant barrier to discovering and exploring new materials. Overcoming this barrier, in this work, we propose a Machine Learning (ML) based technique that can learn inter-atomic potential parameters for various particle-particle interactions employing QM calculations. This ML model can be used as an alternative for QM calculations for predicting non-bonded interactions in a computationally efficient manner. Using these parameters as input to MD simulations, we can predict a diverse range of properties, enabling researchers to design new and novel materials suitable for various applications in the absence of experimental data. We employ our ML-based technique to learn the Buckingham potential, a non-bonded interatomic potential. Subsequently, we utilize these predicted values to compute the densities of four distinct molecules, achieving an accuracy exceeding 93%. This serves as a strong demonstration of the efficacy of our proposed approach.

The development of the ovarian antral follicle is a complex, highly regulated process. Oocytes orchestrate and coordinate the development of mammalian ovarian follicles, and the rate of follicular development is governed by a developmental program intrinsic to the oocyte. Characterizing oocyte signatures during this dynamic process is critical for understanding oocyte maturation and follicular development. Although the transcriptional signature of sheep oocytes matured in vitro and preovulatory oocytes have been previously described, the transcriptional changes of oocytes in antral follicles have not. Here, we used single-cell transcriptomics (SmartSeq2) to characterize sheep oocytes from small, medium, and large antral follicles. We characterized the transcriptomic landscape of sheep oocytes during antral follicle development, identifying unique features in the transcriptional atlas, stage-specific molecular signatures, oocyte-secreted factors, and transcription factor networks. Notably, we identified specific gene and signaling pathways in each antral follicle stage that may reflect oocyte quality and in vitro maturation competency. Additionally, we discovered key biological processes that drive the transition from small to large antral follicles, revealing hub genes involved in follicle recruitment and selection. Thus, our work provides a comprehensive characterization of the single-oocyte transcriptome, filling a gap in the mapping of the molecular landscape of sheep oogenesis. We also provide key insights into the transcriptional regulation of the critical stages of antral follicular development, which is essential for understanding how the oocyte orchestrates follicular development.

Worldwide, hypoxia-related conditions, including cancer, COVID-19, and neuro-degenerative diseases, often lead to multi-organ failure and significant mortality. Oxygen, crucial for cellular function, becomes scarce as levels drop below 10 mmHg (<2% O2), triggering mitochondrial dysregulation and activating hypoxia-induced factors (HiFs). Herein, Oxygen nanoBubbles (OnB), an emerging versatile oxygen de-livery platform, implies to offer a novel approach to address hypoxia-related pathologies. This review explores OnB oxygen delivery strategies and systems, including diffusion, ultrasound, photodynamic, and pH-responsive nanobubbles. It delves into the nanoscale mechanisms of OnB, elucidating their role in mitochondrial metabolism (TFAM, PGC1alpha), hypoxic responses (HiF-1alpha), and their interplay in chronic pathologies including cancer and neurodegenerative disorders, amongst others. By understanding these dynamics and underlying mechanisms, this article aims to contribute to our accruing knowledge of OnB and the developing potential in ameliorating hypoxia- and metabolic stress-related conditions and fostering innovative therapies.

Objective: To observe the effect of the combination of fluid-increasing decoction, low molecular heparin sodium and aspirin in the treatment of oligohydramnios in pregnancy. Methods: In this study, 114 pregnant women with oligohydramnios during pregnancy admitted to our hospital between May 2019 and March 2022 were selected as objects, and the pregnant women were equally divided into the observation group and the experimental group by random number table method, with 57 cases in each group. The observation group received conventional fluid infusion, low molecular heparin sodium and aspirin, while the experimental group was treated with fluid-increasing decoction on the basis of the observation group. The treatment effect, S/D level, amniotic fluid index, maximum vertical pocket (MVP), coagulation indexes (plasma prothrombin time (PT), plasma activated partial thromboplastin time (APTT), fibrinogen (FIB)), pregnancy outcome and adverse reactions were compared between the two groups. Results: The total effective rate of treatment was obviously better in the experimental group than that in the observation group (P＜0.05); the S/D level after treatment in the experimental group was remarkably lower than that in the observation group (P＜0.05). The amniotic fluid index and MVP were remarkably higher in the experimental group than in the observation group after treatment (P < 0.05). No significant differences in PT, APTT and FIB were found between the two groups before and after treatment (P > 0.05). The rate of oligohydramnios at delivery, cesarean section rate, neonatal weight status and preterm delivery rate were dramatically better in the experimental group than in the observation group (P < 0.05). Post-partum haemorrhage rate, neonatal asphyxia rate, amniotic fluid contamination rate and incidence of adverse events were not significantly different between the two groups of pregnant women (P > 0.05). Conclusion: The combination of fluid-increasing decoction, low molecular heparin sodium and aspirin is clinically effective and safe in the treatment of pregnant women with oligohydramnios during pregnancy. The combination is effective in reducing the S/D ratio of fetal umbilical blood flow, enhancing the amniotic fluid index and MVP in pregnant women with oligohydramnios during pregnancy, whilst not adversely influencing the coagulation function of the mother, thus contributing to a reduction in the risk of adverse pregnancy outcomes.

In Pakistan, bats are one of the dominant mammals that play an important role in the ecosystem in terms of pollination, seed dispersal, and control of pest insects. Bats have also played an im-portant role in the emergence and transmission of zoonotic pathogens; however, most current studies focus on viral pathogens, not potential bacterial pathogens. This study was designed to estimate the prevalence and antibiotic profiling of Staphylococcus (S.) aureus in oral and rectal samples from bats captured in northern Pakistan and to determine the factors associated with in-fection. Two hundred individual bats of five species: Pipistrellus javanicus (n = 17), Pipistrellus pipistrellus (n = 10), Rhinopoma microphyllum (n = 48), Rousettus leschenaultii (n = 124), and Scotophilus kuhlii (n = 1) were captured for non-lethal collection of oral and rectal samples to iso-late S. aureus. Bats were sampled from three sites: a natural cave, a man-made castle, and an an-imal shed, in Khyber Pakhtunkhwa and Punjab provinces. Oral (n = 200) and rectal (n = 200) swabs were collected from each individual bat using sterile cotton swabs specifically for use in bacteriological studies. Each isolate of bacteria was identified by using phenotypic tests and con-firmed as S. aureus based on PCR assay. Out of a cumulative four hundred samples, 80 swabs were positive for S. aureus including 47 rectal and 33 oral swabs. Prevalence of S. aureus infection varied significantly among species, with Rousettus leschenaultii exhibiting the highest prevalence (n = 77; 37.90%). In addition to bat species, prevalence varied significantly among habitats but not between sex, age class, or reproductive status. This study confirmed the occurrence of S. aureus in oral and rectal microbiota of bats in Pakistan. Importantly, S. aureus isolates showed resistance to tetracycline, gentamicin, and erythromycin and carried resistant genes such as TetK, TetM, Erma, and aacA-D. In this regard, efforts should be taken to educate the local communities on how to minimize exposure to an antibiotic-resistant bacterial pathogen through contact with bats while simultaneously increasing the awareness of protecting bats as a vital component of our ecosystem.

The emergence of multidrug-resistant pathogens such as Listeria monocytogenes and Shiga toxin-producing Escherichia coli (STEC) poses public health challenges, and this has led to a continuous search for effective novel antimicrobial agents. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria and STEC, and characterize their mechanisms of action. Marine actinoymcetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and tri-fluoroacetoxy hexadecane. SOD(B)ST2SA2`s extract demonstrated the minimum inhibitory con-centration and minimum bactericidal concentration ranging from 0.78–25 mg/ml and 3.13 to > 25 mg/ml, respectively. Diethyl phthalate displayed the lowest bacterial protein binding energies (kcal/mol): −7.2, dihydrofolate reductase; −6.0, DNA gyrase B, and −5.8, D-alanine:D-alanine lig-ase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.

BMAP-27 peptide known to exert cytotoxic effects against cancer cells by membrane integrity disruption. In the current investigation, we aimed to study the role of the BMAP-27 peptide in reducing colon cancer cell proliferation and inducing apoptosis. This study utilized both primary and metastatic colon cancer cell lines (SW480 and SW620). Proliferation was measured using CCK-8, and cellular damage was analyzed by lactate dehydrogenase assay. The study assessed apoptosis, cell cycle, and proliferation by measuring the expression of CASPASE3, BAX, BCL-2, TP53, CDK-6, PCNA, Wnt11, AXIN1, and CTNNB1. Additionally, in-silico studies were conducted to determine the binding affinities of BMAP-27 with APC and β-catenin proteins. BMAP-27 peptide reduced colon cancer cell proliferation, upregulated CASPASE3, BAX, TP53, AXIN1 expression, and downregulated BCL-2, CDK-6, PCNA, WNT11, CTNNB1 in both colon cancer cell lines, however, demonstrated higher activity in primary than metastatic colon cancer cells. The molecular dynamic simulation revealed substantial binding affinity of the peptide to adenomatous polyposis coli and β-catenin proteins.BMAP-27 peptide effectively inhibited the proliferation and enhanced apoptosis in the primary than in metastatic colon cancer cells. In-silico findings suggest that BMAP-27 exhibits a strong binding affinity with APC and β-catenin, highlighting its potential role as an anti-colon cancer agent.

Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain DNA of living cells. To do so, it needs to interact with and permeate through cell membranes. The pH of biological media may vary quite significantly and this influences H33342 ionization state, and may change its rate of permeation through biomembranes. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 &lt; pH &lt; 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics simulations. While probe insertion occurs for all ionization states, with similar overall equilibrium location, orientation was found to depend on the probe charge, with the neutral form lying mostly parallel and the doubly charged displaying a significant tilt relative to the membrane plane. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy of interaction is negative and is larger at lower pH values. This suggests efficient hydrogen bonding between the probe and the lipid, namely for the protonated +2 form. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from water and octanol partition. This highlights the distinction between lipophilicity and hydrophobicity, and the importance of considering association with lipid bilayers when predicting the affinity for biomembranes.

The adsorption of proteins on polymer is widely used in biosensors. Here, molecular dynamics (MD) simulation was used to study the immobilization of angiotensin converting enzyme II (ACE2) with six initial orientations proposed on polystyrene (PS) at the ambient conditions of pH (4.5, 6, 7, 8, 9.5) and NaCl (0.01, 0.05, 0.1, 0.15, 0.2, 0.25 M). ACE2 immobilization under favorable ambient conditions was characterized by minimum distance (short), settlement time (fast), interaction energy (substantial) and protein configuration (stable). ACE2 orientations proposed in 0.15M NaCl were respectively preferable to (90, 0, 0), (0, 0, 0) and (0, 270, 0), (180, 0, 0) and (0, 90, 0), (90, 0, 0) at pH 4.5, 6, 7, 9.5. ACE2 immobilization was further evaluated at pH 7 by optimizing NaCl concentration. Its proposed orientations of (i) (0, 270, 0), (ii) (0, 0, 0) and (90, 0, 0), and (iii) (0, 90, 0) and (90, 0, 0) were preferable in 0.05, 0.1 and 0.2 M NaCl, respectively. The great significance of cubic-orientation settlement mode provides tangible improvement for the microfabrication of biochips for rapid diagnosis of severe acute respiratory syndrome coronavirus II (SARS-CoV-2).

The main objective of this work is to study the effects of carbon nanotubes (CNT) on the strength and electrical properties of cement mortar. Molecular dynamic simulations (MDS) were carried out for the mechanical and electrical properties of the cementitious composite and the associated mechanisms. To model the atomic structure of the Calcium-Silicate-Hydrates (C-S-H) gel, tobermorite 11Å was chosen. Single-walled carbon nanotubes (SWCNTs) embedded in tobermorite structure were tested numerically. In particular, the effect of the concentration of CNT in cement paste was studied. An innovative experiment of electrical characterization of a cementitious composite of carbon nanotubes has been developed.

Due to species barriers and poor adaptability to new host environments, few pathogens cause global pandemics. But, SARS-CoV-2 is one exception with its high transmissivity and delayed onset of symptoms. Fortunately, the world was able to tap on the technologies especially the maturing RT-qPCR designed to combat SARS to launch an initial offensive on SARS-CoV-2. These initial efforts may have bought time for scientists to develop more refined diagnostic tests that specifically target SARS-CoV-2. This article describes the effort put forth by the biotech industry and academia in Singapore to develop diagnostic tests that aid the early detection of positive cases, and thereby help contain the virus. Direct tests such as RT-qPCR and antigen rapid test profile the virus nucleic acid and surface proteins, respectively. But, of equal importance in case detection and treatment is serological tests that measure the relative abundance of IgM and IgG which is indicative of infection phase and quality of immune response in positive cases. Other tests such as isothermal amplification, CRISPR-based diagnostics and breath tests are also in development or at initial field deployment, and would undoubtedly provide valuable use experience useful for the development of molecular assays to detect and combat the next pathogen of global concern.

Peyronie's disease (PD) is a benign condition caused by plaque formation on the tunica albuginea of the penis. It is associated with penile pain, curvature, and shortening, and contributes to erectile dysfunction, which worsens patient quality of life. In recent years, understanding of the detailed mechanisms and risk factors involved in development of PD has been increasing. In this review, the pathological mechanisms and several closely related signaling pathways, including TGF-β, WNT/β-catenin, Hedgehog, YAP/TAZ, MAPK, ROCK, and PI3K/AKT, are described. Findings regarding cross-talk among these pathways are then discussed to elucidate the complicated cascade behind tunica albuginea fibrosis. Finally, various risk factors including genetic involved in the development of PD are presented and their association with the disease summarized. The purpose of this review is to provide better understanding regarding involvement of risk factors in the molecular mechanisms associated with PD pathogenesis, as well as provide insight into disease prevention and novel therapeutic interventions.

Topological indices are invariant numerical fields of a graph that give facts about the structure of graphs and are found to be very helpful in predicting the physical properties of aluminophosphates. The characteristics of the aluminophosphates are similar to those of zeolites. Two examples of current applications are natural gas dehydration and humidity sensor. New frameworks are being synthesised by researchers in chemistry and materials science. There are many layers and holes in these substances. In this study, Vertex version of distance-based topological indices, the entropy of topological indices and their numerical analysis are explained.

Among bryophytes, the Plagiochila genus represents a large group of leafy liverworts, with over 500 species. Plagiochilins A-to-X are sesquiterpenoids isolated from Plagiochila species. The lead compound plagiochilin A (Plg-A), endowed with anticancer and anti-parasitic properties, has been characterized as a potent mitosis inhibitor, acting selectively at the late stage of cytokinesis termed abscission. The compound perturbs the dynamic of microtubules, blocking cell cycle progression and triggering the death of malignant cells. Based on the compound mechanism of action and the analogy with other natural products bearing a dihydro-pyrone moiety, we postulated that Plg-A could bind to the pironetin site of α-tubulin. A molecular docking analysis has been performed to compare binding of all 24 plagiochilins to α-tubulin and to establish structure-binding relationships. The identification of Plg-E and Plg-G as the best binders in the series pointed out to the importance of the C13-OH or C=O group for α-tubulin recognition. This observation led to the testing of the natural product ester plagiochilin A-15-yl n-octanoate and the corresponding alcohol (Plg-OH), both identified as robust α-tubulin binders. The study provides a rational to explain potentially the mechanism of action of Plg-A and to guide the design of new derivatives.

In the course of SARS-CoV-2 infection, the 3CL or nsp5 protease plays a pivotal role as the most important viral protease required for the maturation of viral proteins during host infection. Herein, we simulated for 500 ns 3CLproWT, 3CLproH41A, , 3CLproBeta, and 3CLproOmicron, in complex with the substrates nsp 4|5 and nsp 5|6. Our results show that mutations in the 3CLpro present in the SARS-CoV-2 variant of concerns (VOCs) did not lead to significant conformational changes or changes in substrate binding affinities. However, significantly high cleavage rates for the boundary between nsp4 and nsp5 were obtained for 3CLproBeta and 3CLproOmicron and may play a key role in the viral replication and virus fitness gain. Our molecular dynamics data suggest that the cleavage rate of nsp4|5 may be related to the increased amount of viral load observed for these VOCs, releasing more nsp4 than other non-structural proteins. Based on our hydrogen bonding analyses, we also discovered that Gly143 and Glu166 are key residues in substrate recognition, suggesting that these residues may be incorporated as pharmacophoric centers for Beta and Omicron variants in drug design. Our results suggest that Gly143 and Glu166 are essential residues to interact with Gln6 of the different substrates and, therefore, are potential broad-spectrum pharmacophoric centers of SARS-CoV-2 3CLpro.

Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” axial conformation. Using 13C-labeled InsPs / PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger InsP8 readily adopts both conformations at physiological conditions. Environmental factors - such as pH, metal cation composition, and temperature - strongly influence the conformational equilibrium. Thermodynamic data revealed that the transition of InsP8 from the equatorial to the axial conformation is, in fact, an exothermic process. The speciation of InsPs and PP-InsPs also affects their interaction with protein binding partners; addition of Mg2+ decreased the binding constant Kd of InsP8 to an SPX protein domain. The results illustrate that PP-InsP speciation reacts very sensitively to solution conditions, suggesting it might act as an environment-dependent molecular switch.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have triggered a recent pandemic of respiratory disease and affected almost every country all over the world. A large amount of natural bioactive compounds is under clinical investigation for various diseas-es. Especially, marine natural compounds are gaining more attention in the new drug develop-ment process. The present study has aimed to identify potential marine-derived inhibitors against the target proteins of COVID-19 using a computational approach. Currently, 16 marine clinical-level compounds were selected for computational screening against the four SARS-CoV-2 main proteases. Computational screening resulted from the best drug candidates for each target based on the binding affinity scores and amino acid interactions. Among these, five marine-derived compounds namely Chrysophaentin A (-6.6 kcal/mol), Geodisterol sulfates (-6.6 kcal/mol), Hymenidin (-6.4 kcal/mol), Plinabulin (-6.4 kcal/mol) and Tetrodotoxin (-6.3 kcal/mol) expressed the minimized binding energy and molecular interactions such as covalent and hydrophobic interactions to the SARS CoV-2 Main Protease. Using Molecular dynamic stud-ies, the Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (ROG), and Hydrogen bonds (H-Bonds) values were calculated for SARS-CoV-2 Main Protease with Hymenidin docked complex. Additionally, in silico Druglikeness and pharmaco-kinetic property assessments of the compounds demonstrated favorable druggability. These re-sults suggested that marine natural compounds are capable of fighting SARS-CoV-2. Further, in vitro and in vivo studies need to be carried out to confirm their inhibitory potential.

The factors influencing hepatitis E virus (HEV) circulation remain largely unexplored. We investigated HEV seroprevalence in humans and the prevalence of infection in farm pigs and rabbits in different regions of the Russian Federation, as well as the genetic diversity and population dynamics of HEV. Anti-HEV IgG antibody detection rates in the general population increase significantly with age, from 1.5% in children and adolescents under 20 years old to 4.8% in adults aged between 20 and 59 years old, to 16.7% in people aged 60 years and older. HEV seroprevalence varies between regions, with the highest rate observed in Belgorod Region (16.4% compared with the national average of 4.6%), which also has the country’s highest pig population. When compared with the archival data, both increases and declines in HEV seroprevalence have been observed within the last 10 years, depending on the study region. Virus shedding has been detected in 19 out of the 21 pig farms surveyed. On one farm, circulation of the same viral strain for five years was documented. All human and animal strains belonged to the HEV-3 genotype, with its clade 2 sequences being predominant in pigs. Sequences from patients, pigs, and sewage from pig farms clustered together, suggesting a zoonotic infection in humans and possible environmental contamination. The HEV-3 population size predicted using SkyGrid reconstruction demonstrated exponential growth in the 1970s–1990s, with a subsequent decline followed by a short rise around the year 2010, the pattern being similar to the dynamics of the pig population in the country. The HEV-3 reproduction number (Re) predicted using Birth-Death Skyline analysis has fluctuated around 1 over the past 20 years in Russia, but is 10 times higher in Belgorod Region. In conclusion, HEV-3 circulation varies both geographically and temporally, even within a single country. The possible factors contributing to this variability are largely related to the circulation of the virus among farm pigs.

Non-invasive radionuclide molecular visualization of human epidermal growth factor receptor type 2 (HER2) can provide stratifcation of patients for HER2-targeting therapy. This method can also enable monitoring of the response to such therapies and thereby the treatment will be more personalized and efficient. Phase I clinical evaluation of two scaffold protein-based imaging probes, [99mTc]Tc-(HE)3-G3 and [99mTc]Tc-ADAPT6, demonstrated that their injections are safe, well-tolerated and cause low level of absorbed and equivalent doses. The goal of this preclinical study was to select the best probe for patients’ stratification and for response monitoring. Biodis-tribution of both tracers was compared in mice bearing SKOV-3 xenografts with high HER2 ex-pression and MDA-MB-468 xenografts with very low expression. Changes in accumulation of both probes in SKOV-3 tumors 24 h after injection of trastuzumab were evaluated. Both [99mTc]Tc-ADAPT6 and [99mTc]Tc-(HE)3-G3 permitted high contrast imaging of HER2-expressing tumors and clear discrimination between tumors with high and low HER2 expression. However, [99mTc]Tc-ADAPT6 has better preconditions for higher sensitivity and specificity of stratification. On the other hand, [99mTc]Tc-(HE)3-G3 is capable to sense the decrease of HER2 expression on re-sponse to trastuzumab therapy only 24 h after injection of loading dose. This indicates that this tracer would be better for monitoring early response to such treatment. Results of this study should be considered in planning of further clinical development of HER2 imaging probes.

Background: While mankind is still dealing with the COVID-19 pandemic, on May 7, 2022, a case of monkeypox virus (MPXV) has been reported to the WHO. Monkeypox is a viral zoonotic disease with characteristics comparable to those seen in smallpox cases in the past. It has been a public health threat, particularly in Africa, but recently have been circulating the world, consequently, may become a global public health threat in a very short period. Thus, the current work was planned and then constructed a multi-epitope vaccine that can evoke an immunological response against MPXV utilizing cell surface-binding protein as a target in order to develop a novel vaccine that is both safe and almost free of side effects. Results: The proposed vaccine composed of 304 amino acids and was shown to be antigenic in Vaxijen server (0. 5311) and nonallergenic in AllerTop server. The 3D structure of the designed vaccine is predicted, refined and validated by various in silico tools to assess the stability of the vaccine. Moreover, solubility of the vaccine construct was found greater than the average solubility provided by protein-Sol server indicating the solubility of the vaccine construct. Moreover, the most promising epitopes bound to MHC I and MHC II alleles were found having good binding affinities with low energies ranging between ₋7.0 - ₋8.1kcal/mol. Conclusion: We conclude from our research that the cell surface-binding protein is one of the primary proteins involved in MPXV pathogenesis. The most promising epitopes were selected using a rigorous procedure and used for vaccine design. As a result, our study will aid in the development of appropriate therapeutics and prompt the development of future vaccines against MPXV, which could serve as an important milestone in the production of an antiviral vaccine against MPXV.

Turbulence is a fluid dynamic problem refractory to mathematical treatment. Examining a theoretical model of liquid water flowing in a cylinder at different Raleigh numbers, we propose a novel approach to elucidate the first stages of turbulent flows. The weakly bonded molecular assemblies of liquid water form a fluctuating branched polymer in which every micro-cluster displays different density. Against the common view of liquid water as an incompressible and continuous fluid, we suggest that the occurrence of transient local aggregates could be able to generate the vortices and eddies that are the hallmarks of turbulence. We quantify the local changes in velocity, diameter and density required to engender “obstacles” to the average flow. Then, we show how these microstructures, equipped with different Raleigh numbers and characterized by high percolation index, could generate boundary layers that contribute to micro-vortices production. We conclude that the genesis of turbulence cannot be assessed in terms of collective phenomena, rather is sustained, among many other factors, by the underrated microscopic inhomogeneities of fluids like liquid water.

In previous studies regarding the osseointegration of zirconia (ZrO2) implants, a lack of consistency was observed in the surface topographies of the ZrO2 and Ti samples because of the difficult processability of ZrO2 surfaces. To resolve this problem, we used the molecular precursor method (wet process), which is a surface-modifying technique that can easily change the surface chemistry without changing the surface topography. A roughened Ti surface was prepared using sandblasting (large-grit) and acid treatment. We were able to create ZrO2-coated Ti implants with the same topography as that of roughened Ti substrates using the molecular precursor method, which solution contained a Zr complex. The uniform presence of tetragonal Zr was confirmed, and the apparent zeta potential of the surface of the ZrO2-coated Ti implant was higher than that of Ti. In animal experiments, ZrO2-coated Ti implants showed an equivalent or higher bone-to-implant contact ratio compared to that of the non-coated implants inserted into the femur bone defects of the rats. ZrO2 with the same surface topography as that of roughened Ti exhibits a promotion of osteogenesis equivalent to or better than that of Ti in the early stages of bone formation.

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can provide predictions, reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

Uveal melanoma (UM) is characterized by relatively few, highly incident molecular alterations and their association with metastatic risk is deeply understood. Nevertheless, this knowledge has so far not led to innovate therapies for the successful treatment of UM metastases or for adjuvant therapy, leaving survival after diagnosis of metastatic UM almost unaltered in decades. The driver mutations of UM, mainly in the G-protein genes GNAQ and GNA11, activate the MAP-kinase pathway as well as the YAP/TAZ pathway. At present, there are no drugs that target the latter and this likely explains the failure of MEK-inhibitors. Immune checkpoint blockers, despite the game changing effect in cutaneous melanoma (CM) show only marginal effects in UM probably because of the low mutational burden of 0.5 per megabase and the unavailability of antibodies targeting the main immune checkpoint active in UM. The highly pro-tumorigenic microenvironment of UM also contributes to therapy resistance. However, T-cell redirection by a soluble T cell receptor that is fused to an anti-CD3 single-chain variable fragment, local, liver specific therapy, new immune checkpoint blockers and YAP/TAZ specific drugs give new hope to repeat the success of innovative therapy obtained for CM.

Agaricus bisporus is belonging to family agaricaceae, which is widely acceptable and mostly cultivated among the all mushrooms. It has great nutritional values and it is rich in proteins, vitamins, carbohydrates, fibers, minerals and amino acids. It is effective in antimicrobial, anticancer, antidiabetic, antihypercholesterolemic, antihypertensive, hepatoprotective and antioxidant activities. As it is effective in anticancer property, we check the effects of chemical constituents of Agaricus Bisporus on DNA damaging protein which results its activity PARP inhibiting or vise-versa. We choose the molecular docking technique to check the effects of different chemical constituents of Agaricus Bisporus on DNA damaging protein. For that different PARP inhibitory drugs taken as the standard. We perform the molecular docking of the chemical constituents of Agaricus Bisporus, using 4UND protein with the help of PyRx software and BIOVIA Discovery studio software. Along with that PARP inhibitor drugs also run against the same protein. The results of molecular docking shows the some of the constituents of Agaricus Bisporus has better binding affinity than the standard taken PARP inhibitor drugs. The ergosterol shows the better binding affinity than the niraparib and rucaparib on the same proteins. On other hands the naringenin, quercetin, anthocyanin, folate and myricetin shows the better results than the rucaparib. That means the ergosterol shows the better results as PARP inhibitor than the niraparib and rucaparib.

Abstract: In 2016, we conducted an entomological survey in a railway transect between Banfora and Ouagadougou, Burkina Faso. The aim was to evaluate the risk factors for arbovirus epidemics, including vector infection status, in areas representative of the country. Aedes aegypti mosquitoes were collected at larval stage from four study sites and reared until adult stage and kept in RNAlater for detection of arbovirus RNA. In the laboratory, the mosquito specimens were screened for dengue virus (DENV) and chikungunya virus (CHIKV) using one step real-time qRT-PCR. We detected one DENV-2 positive pool from Ouagadougou, giving a minimum infec-tion rate (MIR) of 16.67, and 6 CHIKV positive pools, giving a MIR of 66.67 from Ouagadougou, but also in Banfora and Boromo. The qRT-PCR is a useful tool for the surveillance of arboviruses of public health importance in Burkina Faso and may be incorporated into disease surveillance and control programs in Burkina Faso.

We present a critical analysis of the mechanism of reversible hydrogen evolution reaction based on thermodynamics of hydrogen processes considering atomic and ionic species as intermediates. Clear distinction between molecular hydrogen evolution/oxidation (H$_2$ER and H$_2$OR) and atomic hydrogen evolution/oxidation (HER and HOR) reactions is made. It is suggested that the main reaction describing reversible H$_2$ER and H$_2$OR in acidic and basic solutions is: $\ce{H3O^+} + 2e^- \xrightleftharpoons{\mathrm{({H}_{2}^{+}})_{ad}} \ce{H2} + \ce{OH^-}$, which proceeds via the formation of hydrogen molecular ion as intermediate and its potential is $E^{0}$ = 0.414~V (at the standard Hydrogen electrode SHE scale). We analyse experimentally reported data with models which provide \emph{quantitative} match (R.J.Kriek et al., Electrochem. Sci. Adv. e2100041 (2021)). The experimentally observed slope of $\lg(Current)$ vs. $Potential$ equal to $\approx 30$~mV/dec corroborates the presented model of H$_2$ER/H$_2$ER based on \ce{H2$^+$} as intermediate.

The synthesis of additives for thinning mineral suspensions based on sodium polyacrylate was carried out. The effect of molecular weight regulators on the molecular weight characteristics of the polymer and the effect of such polymers on the rheological properties of suspensions was studied. Sodium acrylate polymers are synthesized by free radical polymerization in aqueous solution using molecular weight regulators. The molecular weight characteristics of the polymeric samples were estimated by viscometry using Mark-Houwink-Kuhn-Sakurada (MHKS) equation. Synthesized polymers were used as thinners ceramic slurries, prepared according to the recipe of the enterprises producing ceramic products. The thinning ability of polymer samples with different molecular weights was estimated using an Engler viscometer from the time of the ceramic slurry flow. The influence of the type and amount molecular weight regulator on polyacryates was revealed. It was found that molecular weight synthesized samples was in the range of 21000 - 91000. It was determined that samples with a molecular weight of 28000 - 35000 synthesized using mercaptoethanol (at a dosage of 0.5-1.5% by weight of the monomer) provide optimal fluidity to the ceramic slurry.

The [3+2] cycloaddition (32CA) reactions of strongly nucleophilic norbornadiene (NBD) with simplest diazoalkane (DAA) and three DAAs of increased electrophilicity have been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. These pmr-type 32CA reactions follow an asynchronous one-step mechanism with activation enthalpies ranging from 17.7 to 27.9 kcal·mol-1 in acetonitrile. The high exergonic character of these reactions makes them irreversible. The presence of electron-withdrawing (EW) substituents in the DAA increases the activation enthalpies, in complete agreement with the experimental slowing-down of the reactions, but contrary to the Conceptual DFT prediction. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather non-polar 32CA reactions. The present MEDT study allows establishing that the depopulation of the NNC core in this series of DAAs with the increase of the EW character of the substituents present at the carbon center is responsible for the experimentally found deceleration.

Molecular mechanisms for N2 fixation (solar NH3) and CO2 conversion to C2+ products in enzymatic conversion (Nitrogenase), electrocatalysis, metal-complexes and plasma-catalysis are analysed and compared. It is evidenced that differently from what present in thermal and plasma-catalysis, the electrocatalysis path requires not only the direct coordination and hydrogenation of undissociated N2 molecule, but to realize a series of features present in the Nitrogenase mechanism. There is the need of i) a multi-electron and -proton simultaneous transfer, not as sequential steps, ii) forming bridging metal hydride species, iii) generate intermediates stabilized by bridging multiple metal atoms, iv) have the capability of the same sites to be effective both in N2 fixation and in COx reduction to C2+ products. Only iron oxide/hydroxide stabilized at defective sites of nanocarbons was found to have these features. This comparison of the molecular mechanisms in solar NH3 production and relations with CO2 reduction is proposed to be a source of inspiration to develop the next generation electrocatalysts to address the challenging transition to a future sustainable energy and chemistry beyond fossil fuels.

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

The world faces two seemingly unrelated challenges—a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.

Evaporation studies of water using classical molecular dynamics simulations are largely limited due to its high computational expense. We aim at addressing the computational issues by developing a coarse grain model for evaporation of water on solid surfaces by combining four water molecules into a single bead. Most commonly used mono atomic pair potentials like Lennard Jones, Morse, Mie and three body potential like Stillinger-Weber are optimized using a combination of Genetic algorithm and Nelder-Mead algorithm. Among them, Stillinger-Weber based model shows excellent agreement of density and Enthalpy of vaporization with experimental results for a wide range of temperatures. Further, the new water model is used to simulate contact angle of water and thin film evaporation from surfaces with different wettabilities.

Metabolic enzymes are often targeted for drug development programs of metabolic diseases such as diabetes and its complications. Many secondary metabolites isolated from natural products have shown therapeutic action against these enzymes. However, some commercially available synthetic drugs have shown unfriendly impacts with various side effects. Thus, this research has focused on a comprehensive study of secondary metabolites showing better inhibitory activities towards metabolic enzymes such as α-amylase, α-glucosidase, aldose reductase, and lipase. Further receptor-based virtual screening was performed against the various secondary metabolites database designed in-silico. Using Gold combined with subsequent post-docking analyses, the score was obtained as methyl xestospongic ester (Gold score 65.83), 2,″4″-O-diacetylquercitrin (Gold score 65.15), kaempferol-3-O-neohesperidoside (Gold score 53.37) and isosalvianolic acid C methyl ester (Gold score 53.44) for lipase, aldol reductase, α-amylase, and α-glucosidase, respectively. Besides, vitexin and isovitexin for α-amylase; N-trans-Caffeoyl-tyramin for α-glucosidase; purpurolide F and schaftoside for lipase; acteoside and orientin for aldose reductase could be potential drugs for respective enzymes based on in-silico analyses, supported by experimental IC₅₀ values reported. They could bind to the competitive sites of the various targets of metabolic enzymes, and finally, toxicity analysis using ProTox-II was also performed.

Never in mitosis gene A-related kinase 2 (NEK2) a member of serine-threonine kinase protein mainly involved in the cell cycle process. Clinical studies revealed NEK2 overexpression in various tumour types, also NEK2 was reported for their association with genetic abnormalities like mitotic machinery deregulation and chromosomal instability. Besides NEK2 plays a key role in maintaining the transformed phenotype of cancer cells and chemo-resistance of several tumour types. Thus, NEK2 transcriptional profile is important for diagnosis, treatment, and prognosis stages of cancer studies. Screening of novel NEK2 inhibitor would be beneficial in developing the specific lead molecules. Our studies involved NEK2 transcriptional profile search, screening of druggable cavities in NEK2, Drug likeliness of mangrove derived naphthoquinone derivatives avicennoneA , avicennoneB , avicennoneC , avicennoneD , avicenoneE , avicennone F , and avicennone G , avicequinone A, stenocarpoquinone B , avicequinone C , avicenol A , avicenol C,brugine, apigenin, chrysin and molecular docking studies to assess MNC compounds binding efficacy towards NEK2. Mangrove derived compounds conferred the intermolecular hydrogen bond, Pi-alkyl,pi-cation interactions with NEK2 kinase domain region residues Tyr 19, Lys 37, Arg 164, Lys174. Nearly 200 kinase proteins contained this promising Cys 22 residue as its positioned in the catalytic site like NEK family proteins. Avicenna A, Avicennone G, Chrysin and Brugine formed the irreversible covalent binding with NEK2 through Cys 22, thus they can be considered as potential kinase inhibitors with the limited off-target response. But these MNC compounds need to be tested further in invitro and invivo studies to propose as potent NEK2 inhibitors.

Introduction: Coronaviruses are zoonotic viruses that include human epidemic pathogens such as the Middle East Respiratory Syndrome virus (MERS-CoV), and the Severe Acute Respiratory Syndrome virus (SARS-CoV), among others (e.g., COVID-19, the recently emerging coronavirus disease). The role of animals as potential reservoirs for such pathogens remains an unanswered question. No systematic reviews have been published on this topic to date. Methods: We performed a systematic literature review with meta-analysis, using three databases to assess MERS-CoV and SARS-CoV infection in animals and its diagnosis by serological and molecular tests. We performed a random-effects model meta-analysis to calculate the pooled prevalence and 95% confidence interval (95%CI). Results: 6,493articles were retrieved (1960-2019). After screening by abstract/title, 50 articles were selected for full-text assessment. Of them, 42 were finally included for qualitative and quantitative analyses. From a total of 34 studies (n=20,896 animals), the pool prevalence by RT-PCR for MERS-CoV was 7.2% (95%CI 5.6-8.7%), with 97.3% occurring in camels, in which pool prevalence was 10.3% (95%CI 8.3-12.3). Qatar was the country with the highest MERS-CoV RT-PCR pool prevalence, 32.6% (95%CI 4.8-60.4%). From 5 studies and 2,618 animals, for SARS-CoV, the RT-PCR pool prevalence was 2.3% (95%CI 1.3-3.3). Of those, 38.35% were reported on bats, in which the pool prevalence was 14.1% (95%CI0.0-44.6%). Discussion: A considerable proportion of infected animals tested positive, particularly by nucleic acid amplification tests (NAAT). This essential condition highlights the relevance of individual animals as reservoirs of MERS-CoV and SARS-CoV. In this meta-analysis, camels and bats were found to be positive by RT-PCR in over 10% of the cases for both; thus, suggesting their relevance in the maintenance of wild zoonotic transmission.

Bitter gourd is an important vegetable of the family Cucurbitaceae, cultivated mainly in humid and subtropical Asia. Bitter gourd is vegetable with immense health benefits due to the presence of medicinal compounds such as charatin, vicine, and polypeptide-p, which play an essential role in lessening the blood glucose levels. Moreover, bitter gourd fruits are particularly rich in vitamin C, minerals, and carotenes. Here, an effort has been made to critically evaluate the extent of achievements during the enhancement and enactment of bitter gourd breeding programs with the use of latest technologies. Broadening of the genetic base of cultivated bitter groud varieties as a result of enrichment of the existing resources by using the wild species in the breeding programs. Practical seed production technological know-how along with the use of the MS system (male sterility)/chemical-induced sterility procedure is nonetheless vital to cope up with the market demands. Superior yielding bitter gourd hybrids combining early maturity and resistance to biotic and abiotic stresses are regularly needed to cope up with the challenge of bitter gourd production.

Around the World, the number of compound databases of natural products in the public domain is rising. This is in line with the increasing synergistic combination of natural product research and chemoinformatics. Towards this global endeavor, countries in Latin America are assembling, curating, and analyzing the contents and diversity of natural products available in their geographical regions. In this manuscript we collect and analyze the efforts that countries in Latin America have made so far to build natural product databases. We further encourage the scientific community in particular in Latin America, to continue their efforts to building quality natural product databases and, whenever possible, to make them publicly accessible. It is proposed that all compound collections could be assembled into a unified resource called LANaPD: Latin America Natural Products Database. Opportunities and challenges to build, distribute, and maintain LANaPD are also discussed

The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the world health organization declared it pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. In this urgency situation, development of SARS-CoV-2 based vaccines is immediately required. Immunoinformatic and molecular modelling are generally used time-efficient methods to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines is proved to be a promising immunization strategy against viruses and pathogens, which induce more comprehensive protective immunity. The current study demonstrated a comprehensive in-silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in-silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in E. Coli. Despite this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can present to be a better prophylactic solution against COVID-19.

Malignant gliomas are heterogeneous neoplasms. Glioma stem-like cells (GSCs) are undifferentiated and self-renewing cells that develop and maintain these tumors. These cells are the main population that resist current therapies. Genomic and epigenomic analyses has identified various molecular subtypes. Bone morphogenetic protein 4 (BMP4) reduces the number of GSCs through differentiation and induction of apoptosis, thus increasing therapeutic sensitivity. However, the short half-life of BMP4 impedes its clinical application. We have previously reviewed BMP4 signaling in central nervous system development and glioma tumorigenesis and its’ potential as a treatment target in human gliomas. Recent advances in understanding both adult and pediatric malignant gliomas highlight critical roles of BMP4 signaling pathways in the regulation of tumor biology, and indicate its’ potential as a therapeutic molecule. Furthermore, significant progress has been made on synthesizing BMP4 biocompatible delivery materials, which can bind to and markedly extend BMP4 half-life. Here, we review current research associated with BMP4 in brain tumors, especially in pediatric malignant gliomas. We also summarize BMP4 delivery strategies, with a focus on biocompatible BMP4 binding peptide amphiphile nanostructures as promising novel delivery platforms for treatment of these devastating tumors.

I demonstrate that the ionization energy (IE) and the electron affinity (EA) of organic molecular crystals can be predicted from first-principles. Here, I describe the induced electronic polarization and the electrostatic effects upon crystalline IE and EA. I also demonstrate that the electronic polarization mainly originates from the screened coulomb interaction inside the crystalline bulk phase, and that the electrostatic contribution to IE and EA crucially depends on the orientation of the molecule at the surface. The former is well described by the GW approximation, while the latter is reasonably estimated by the difference in frontier orbital energy between the gas phase and the surface at the level of a generalized gradient approximation to the density functional theory. The present methodology enables to demonstrate the impact of the electrostatic effect upon the energy level of the injected charge at a multi-monolayer surface of an organic semiconductor thin film.

Excitotoxicity related to the dysfunction of the N-methyl-d-aspartate receptor (NMDAR) has been indicated to play an integral role in the pathophysiology of multiple disease states, including neurodegenerative disorders such as Parkinson’s disease. There is a notable gap in the market for novel NMDAR antagonists, however current methods to analyze potential antagonists rely on indirect measurements of calcium flux and hazardous radioligand binding assays. Recently, a fluorescent NMDAR ligand, N-adamantan-1-yl-dimethylamino-1-naphthalenesulfonic acid, known as AM-DAN was developed by our group. Additional studies on this ligand is necessary to evaluate its potential as a biological tool in NMDAR research. Therefore, this study was aimed at conducting structural analyses, fluorescence experiments, high-accuracy NMDAR molecular modelling and NMDAR phencyclidine (PCP) site competition binding studies using AM-DAN. Results revealed that AM-DAN has appropriate structural properties, significant fluorescent ability in various solvents and is able to bind selectively and compete for the PCP-binding site of the NMDAR. Therefore, AM-DAN holds promise as a novel fluorescent ligand to measure the affinity of prospective drugs binding at the NMDAR PCP-site and may circumvent the use of radioligands.

Molecular dynamics(MD) simulations are carried out to characterize the mechanicalproperties and failure behavior of van der Waals heterostructures composed ofgraphene and hexagonal boron nitride(hBN) single layer sheets. The graphene–hBNand hBN–graphene–hBN heterostructures simulations are carried out under tensileand shear deformation. Accordingly, stress versus strain curves of each systemare plotted and various properties of heterostructures, namely elastic modulusand shear modulus as well as failure stress and failure strain, are evaluatedand compared with one another as well as with the pristine graphene and hBNsheets. Subsequently, the failure mechanism/characterization of each sheet in theheterostructures is described. Alternatively, the elastic and shear modulus of eachheterostructure are computed by means of rule of mixture(ROM) which are in goodagreement with results that are obtained from MD simulations.

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Binderless zeolite macrostructures in the form of ZK-4 microspheres were prepared using anion exchange resin beads as shape directing macrotemplates. The particles were synthesized under hydrothermal conditions at different temperatures and treatment times. The influence of the different synthesis parameters was investigated by X-ray diffraction, scanning electron microscopy, fluorescence X, nitrogen adsorption measurements and ²⁹Si solid NMR. Fully crystalline spheres similar in size and shape to the original resin beads were obtained by a hydrothermal treatment at the highest temperatures (150 - 180 °C) for a short treatment time of 24 h. The synthesized microspheres showed to be promising in the molecular decontamination of Volatile Organic Compounds (VOCs).

This work examines atomic and molecular signatures in laser-induced plasma in standard ambient temperature and pressure environments, including background contributions to the spectra that depend on the laser pulse-width. Investigations include solids, gases, and nano-particles. Abel inversions of measured line-of-sight data reveal insight into the radial plasma distribution. For nominal 6 nanosecond laser pulses and for pulse-energies in the range of 100 to 800 milli-Joules, expansion dynamics and turbulence due to shock phenomena are elucidated to address local equilibrium details that are frequently assumed in spatially averaged emission spectroscopy. Chemical equilibrium computations reveal temperature dependence of selected plasma species. Specific interests include atomic hydrogen (H) and cyanide (CN). The atomic H spectra, collected following optical breakdown in ultra-high-pure hydrogen and 9:1 mixtures of ultra-pure hydrogen and nitrogen gases, indicate spherical shell structures and isentropic expansion of the plasma kernel over and above the usual shockwave. The recombination radiation of CN emanates within the first 100 nanoseconds for laser-induced breakdown in a 1:1 CO₂:N₂ gas mixture when using nanosecond laser pulses to create the micro-plasma. The micro-plasma is generated using 1064 nm, 150 mJ, 6 ns Q-switched Nd:YAG laser radiation. Measurements of the optical emission spectra utilize a 0.64 m Czerny-Turner type spectrometer and an intensified charge-coupled device.

The present study examined and compared the effects of high- and low-molecular weight (MW) chitosan, a nutraceutical, on intestinal and liver lipid metabolism in rats fed with high-fat diet. Both high- and low-MW chitosan decreased liver weight, elongated small intestine, improved the dysregulation of blood lipids and liver fat accumulation, and increased fecal lipid excretion in high-fat diet-fed rats. Supplementation of both high- and low-MW chitosan significantly inhibited the decreased phosphorylated AMP-activated protein kinase (AMPK)α and peroxisome proliferator-activated receptor (PPAR)α protein expressions and the increased lipogenesis/cholesterogenesis-associated protein expressions (sterol regulatory element binding protein (SREBP)1c, SREBP2, and PPARγ) and the decreased apolipoprotein (Apo)E and microsomal triglyceride transfer protein (MTTP) protein expressions in the livers of high-fat diet-fed rats. Both high and low-MW chitosan supplementation could also suppress the increased MTTP protein expression and the decreased angiopoietin-like protein (Angptl)4 protein expression in the intestines of high-fat diet-fed rats. Comparison between high and low-MW chitosan, high-MW chitosan has a higher efficiency than low-MW chitosan on the inhibition of intestinal lipid absorption and the increase of hepatic fatty acid oxidation, which can improve liver lipid biosynthesis and accumulation.

Structural DNA nanotechnology provides an excellent foundation for diverse nanoscale shapes that can be used in various bioapplications and materials research. From all existing DNA assembly techniques, DNA origami has proven to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA has drastically advanced, and therefore, more and more complex DNA-based systems have become accessible. So far, vast majority of the demonstrated DNA origami frameworks are static by nature, but interestingly, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that perform controlled translational or rotational movement triggered by predefined DNA strands, various molecular interactions and/or other external stimuli such as light, pH, temperature and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular scale precision measurements, targeted drug delivery and diagnostics, but they can also play a role in development of optical/plasmonic sensors, nanophotonic devices and nanorobotics for numerous different tasks.

We performed for the first time to our knowledge fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions. We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm. The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation. We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier.

Effect of abrasive shape on the three-body abrasion behaviors of monocrystalline silicon was investigated by Molecular dynamics modelling. The axial ratio of abrasive particle was varied from 1.00, i.e., a complete sphere, to 0.40 to mimic abrasive shape. The particle’s movement turns toward sliding from rolling when the axial ratio becomes less than a critical value 0.46. In the abrasion process, the friction force and normal force showed an approximately sinusoid-like fluctuation for the rolling ellipsoidal particles, while the front cutting of particle caused that friction force increased and became larger than normal force for sliding particles. The phase transformation process was tracked under different particle’ movement patterns. The Si-II and Bct5 phase producing in loading process can partially transform to Si-III/Si-XII phase and backtrack to original crystal silicon under pressure release, which also occurred in the abrasion process. The secondary phase transformation showed difference for particles’ rolling and sliding movements after three-body abrasion. The rolling of particle induced the periodical and inhomogeneous deformation of substrates, while the sliding benefited producing high-quality surface in CMP process. This study aiming to construct more precise model to understand the wear mechanism benefits evaluating the MEMS wear and CMP process of crystal materials.

The mesoporous heteroatom molecular sieve MCM-41 bulk crystals with the crystalline phase were synthesized via a one-step hydrothermal method using an ionic complex as template. The ionic complex template was formed by interaction between cetyltrimethylammonium ions and metal complex ion [M (EDTA)]2- (M=Co or Ni ). The materials were characterized by X-ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, N2 adsorption–desorption isotherms, and X-ray absorption fine structure spectroscopy. The results showed that the materials possess a highly ordered mesoporous structure with the crystalline phase and possess high uniform ordered arrangement channels. The structure is in the vertical cross directions with a crystalline size of about 12 µm and high specific surface areas. The metal atoms were incorporated into the zeolite frameworks in the form of octahedral coordinate and have a uniform distribution in the materials. The amount of metal complexes formed by metal ion and EDTA is an essential factor for the formation of the vertical cross structure. Comparing to Si-MCM-41, the samples exhibited better conversion, higher selectivity for cumene cracking.

Diabetes mellitus is the fifth deadliest disease in the developing countries. Even with all the research and new drugs available, combating diabetes is still challenging. There are successes in finding new cost effective drugs without side effects, even if not perfect. In our investigation we studied binding mechanism of secondary metabolite of T. chebula in silico. It was observed that three compounds out of 16 have a higher binding affinity for the target proteins. Ellagic acid showed highest binding affinity with alpha amylase, beta glucosidase and alpha glucosidase with lesser binding energies -4.5kcal/mol, -5.36kcal/mol and -4.48kcal/mol respectively. Arjungenin has lesser binding energy of 4.77 kcal/mol with glucokinase while luteoline has binding energy of -7.25kcal/mol for enzyme glycogen synthase kinase. These entire compounds interacted with non-covalent interaction. Petroleum ether extract showed the significant alpha amylase inhibitory activity i.e. 51.22% as compared to standard drug (65.99%).TLC analysis revealed the presence of total 9 compounds in different plant extracts one of them might be a lead compound which could be further exploited for the development of novel safer and potent antidiabetic drug.

The new coronavirus SARS-CoV-2 is the cause of the COVID-19 pandemic, which has created an incomparable global health problem. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. The review begins by elucidating the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Employing homology modeling, a tertiary structure model of PLpro is constructed, laying the groundwork for subsequent investigations. To expedite the search for potential therapeutic candidates, the study harnesses computational methodologies. Molecular docking techniques are employed to explore binding sites for antiviral drugs within the catalytic region of PLpro. This computational approach not only aids in drug development but also provides crucial preliminary data before experimental research commences. The stability of drug-PLpro complexes is assessed through comprehensive all-atom molecular dynamics (MD) simulations, affording dynamic insights into drug-PLpro interactions. By evaluating binding energy estimates from MD simulations, stable drug-PLpro complexes with potential antiviral properties are identified. However, it is emphasized that experimental validation is imperative to confirm these computational findings, necessitating in vitro and in vivo tests to assess safety and efficacy. This pivotal stage bridges the computational realm with real-world clinical applications. The review emphasizes the imperative need for enhancements in the existing PLpro-targeting drugs currently on the market. Their actions are insufficient for clinical use and necessitate thorough characterization and improvement. The Supervised Molecular Dynamics (SuMD) simulation technique reveals critical information about drug unbinding pathways, shedding light on opportunities for refinement. In addition to optimizing existing drugs, the investigation of sub-structurally similar molecules emerges as a promising avenue for drug development. In conclusion, the review underscores the pivotal role of targeting SARS-CoV-2 PLpro in the ongoing battle against COVID-19. By integrating molecular dynamics simulations, structural modeling, and computational insights, a robust foundation is established for identifying promising antiviral drug candidates. The continual need for improvement in existing drugs and the exploration of novel compounds remain paramount in the global effort to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, illustrating the interdisciplinary synergy crucial to this endeavor.

The electronic structure and the participation of the simplest azomethine imine (AI) in [3+2] cycloaddition (32CA) reactions have been analysed within the Molecular Electron Density Theory (MEDT) using DFT calculations at the MPWB1K/6-311G(d) level. Electron localisation function (ELF) topological analysis reveals that AI has a pseudoradical structure, while the conceptual DFT reactivity indices characterise this TAC as a moderate electrophile and a good nucleophile. The non-polar 32CA reaction of AI with ethylene takes place through a one-step mechanism with low activation energy, 5.3 kcal/mol-1. A bonding evolution theory (BET) study indicates that this reaction takes place through a non-concerted [2n+2τ] mechanism in which the C–C bond formation is clearly anticipated prior to the C–N one. On the other hand, the polar 32CA reaction of AI with dicyanoethylene takes place through a two-stage one-step mechanism. Now, the more favourable regioisomeric transition state structure (TS) is located 8.5 kcal•mol⁻¹ below the reagents, in complete agreement with the high polar character of the TS. The current MEDT study makes it possible to extend Domingo’s classification of 32CA reactions to a new pra-type of reactivity.

A better understanding of high temperature processes in slags contributes to facilitate knowledge based design of the solidified product. Here, a slag analogue with a nominal composition of 17 wt% LiMnO2 and 83 wt% Ca2SiO4 was synthesized encountering fairly high cooling rates. The Mn species from 1223 K to 1773 K was simulated using a thermodynamic model assuming a homogeneous melt. The micro-composition including the Mn species of the solidified slag was determined experimentally and was used as basis for molecular dynamics (MD) simulation. The MD simulation provides information on structure and viscosity at high temperatures, otherwise difficult to access. These parameters significantly influence oxidation state of redox-active elements and the solidified product. The micro-composition analyzed by electron probe micro analysis (EPMA) and synchrotron based micro-X-ray fluorescence (micro-XRF) showed that Mn-rich and Ca-Si-rich phases are separated. While the Mn-O phases did not contain noticeable Ca, the Ca2SiO4 phase had incorporated 0.6 wt% of Mn. The slag solidified into round shaped and droplet shaped grains of a Li-Mn-oxide, some Mn3O4 and Ca2SiO4. The powder X-ray diffraction (PXRD) confirmed the formation of larnite, the identity of the Li-Mn-oxide however remained inconclusive. The Mn oxidation state (OS) was identified using synchrotron based micro-X-ray absorption near edge spectroscopy (micro-XANES). The Mn-O grains, matched well with Li-Mn-oxides and a Mn OS: +3 e.g. LiMn3+O2. Small areas matching Hausmannite (Mn2+Mn23+O4) were also identified. The OS of Mn in the silicate phase could not be identified. For comparison a slowly cooled slag analogue with similar composition however higher Si content, was also subjected to micro-XANES. The slowly cooled slag formed long Mn-rich needles in a matrix of large calcium silicate crystals. The Mn-rich crystals matched well with the XANES spectrum of a Mn3+ Li-oxide like LiMn3+O2. At the rim of the needles the Mn-spectra matched well the Hausmannite (Mn2+Mn23+O4) reference. In the silicate phases Mn had a OS: +2, unambiguously. The melt structure at different temperatures of two compositions i.e. LiMn3+O2 and Ca2SiO4 was simulated using molecular dynamics (MD). They serve as model compositions assuming a heterogeneous melt. The results show significant different degrees of polymerization and viscosity. Information from MD simulations can support the identification of potentially different oxygen permeability and with that prediction of oxidation states. The bulk composition was identified by inductively coupled plasma optical emission spectrometry (ICP-OES), bulk structure by PXRD and bulk species by lab-XANES. The synchrotron micro analysis including micro-XRD were performed at the microfocus beamline I18 at the Diamond Light Source. Pure reference compounds were prepared and characterized with the same multi-modal approach.

CO2 geological sequestration in coal seams can achieve the dual objectives of CO2 emission reduction and enhanced coalbed methane production, making it a highly promising carbon capture and storage technology. However, the injection of CO2 into coal reservoirs in the form of supercritical fluid (ScCO2) leads to complex physicochemical reactions with the coal seam, altering the properties of the coal reservoir and impacting the effectiveness of CO2 sequestration and methane production enhancement.In this paper, theoretical calculations based on ReaxFF-MD were conducted to study the interaction mechanism between ScCO2 and the macromolecular structure of both low-rank and high-rank coal, to address the limitations of experimental methods. The reaction of ScCO2 with low-rank coal and high-rank coal exhibits significant differences. At swelling stage, the low-rank coal experiences a decrease in aromatic structure and aliphatic structure, high-rank coal shows an increase in aromatic structure and a decrease in aliphatic structure, while swelling phenomenon is more pronounced in high-rank coal. At dissolution stage, low-rank coal is initially decomposed into two secondary molecular fragments, and then recombine to form new molecular structure, the aromatic structure increased and the aliphatic structure decreased. In contrast, high-rank coal occurs stretches-breakage-movement-reconnection, a reduction in aromatic structure and an increase in aliphatic structure.The primary reasons for these variations lie in distinct molecular structure compositions and the properties of ScCO2, leading to different reaction pathways of functional group and aromatic structure. The reaction pathways of functional groups and aromatic structures in coal can be summarized as follows: the breakage of the O-H bond in hydroxyl groups, the breakage of the C-OH bond in carboxyl groups, transformation of aliphatic structures into smaller hydrocarbon compounds or formation of long-chain alkenes, and various pathways involving broken, rearrangement, recombination of aromatic structures. In low-rank coal, there is a higher abundance of oxygen-containing functional groups and aliphatic structures. The breakage of O-H and C-OH chemical bonds results in the formation of free radical ions, while some aliphatic structures detach to produce hydrocarbons. Additionally, some of these aliphatic structures combine with carbonyl groups and free radical ions to generate new aromatic structures. Conversely, in high-rank coal, the lower content of oxygen-containing functional groups and aliphatic structures, along with stronger intramolecular forces, results in fewer chemical bond breakages and makes it less conducive to the formation of new aromatic structures.These results elucidate the specific deformations of different chemical groups, offering a molecular-level understanding of the interaction between CO2 and coal.

The efficacy and cost-effectivness of Multigene Panel Next-Generation Sequencing (NGS) in directing patients towards genomically matched therapies remains uncertain. This study investigated metastatic colorectal cancer (mCRC) patients who underwent NGS analysis on formalin-fixed paraffin-embedded tumor samples. Data from 179 patients were analyzed, revealing no mutations in 39 patients (21.8%), one mutation in 83 patients (46.4%), and two or more mutations in 57 patients (31.8%). KRAS mutations were found in 87 patients (48.6%), including KRAS G12C mutations in 5 patients (2.8%), PIK3CA mutations in 40 patients (22.4%), BRAF mutations in 26 patients (14.5%). Less common mutations were identified: ERBB2 in 5 patients (2.8%) and SMO in 4 patients (2.2%). Additionally, MAP2K1, CTNNB1, and MYC were mutated in 3 patients (2.4%). Two mutations (1.1%) were observed in ERBB3, RAF1, MTOR, JAK1, and FGFR2. No significant survival differences were observed based on mutation numbers. 40% of patients had druggable molecular alterations, but only 1.1% received genomically guided treatment, suggesting limited application in standard practice. Despite this, expanded gene panel testing can identify actionable mutations, aiding personalized treatment strategies in metastatic CRC, although current eligibility for biomarker-guided trials remains limited.

Asymmetric lithium salts, such as Lithium (difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide (LiDFTFSI), have been demonstrated to surpass traditional symmetric lithium salts with improved Li+ conductivity and the capacity to generate stable solid electrolyte interphase (SEI) while maintaining compatibility with aluminum (Al0) current collector. However, the intrinsic reductive mechanism through which LiDFTFSI influences battery performance remains unclear and under debate. Herein, the detailed SEI reactions of LiDFTFSI-based electrolytes were investigated by combining density functional theory and molecular dynamics, aiming to clarify the formation process and atomic structure of SEI. Our results show that asymmetric DFTFSI– weakens the interaction between carbonate solvents and Li+, and substantially alter the solvation structure, exhibiting a well-balanced coordination capacity to bis(trifluoromethanesulfonyl)imide (TFSI–). Nanoseconds hybrid molecular dynamics simulation further reveals that the preferential decomposition of LiDFTFSI produces sufficient LiF and Li2O to facilitate a robust SEI. Moreover, the abundant F– generated from LiDFTFSI decomposition accumulates on the Al surface and subsequently combines with Al3+ from the current collector to form AlF3, potentially inhibiting corrosion of the current collector. Overall, these findings elucidate how LiDFTFSI regulates the solvation sheath and SEI structure, advancing the development of high-performance electrolytes compatible with current collector.

Morphological and phylogenetic (45S nrDNA+RPB1 gene) analyses of three glomoid spore-producing arbuscular mycorrhizal fungi revealed the presence of two new species be-longing to the genus Glomus in the family Glomeraceae. In the field, Glomus highlandensis sp. nov. was found in a saltmarsh of the Scottish Highlands and in maritime sand dunes of the Baltic Sea in Poland, both saline environments, while G. mongioie sp. nov. originates from the Italian Alps. Phylogenetic placement analysis using environmental sequences indicated that G. highlandensis could have likely worldwide distribution while G. mongioie seems to be a rare species in the world. The molecular and phylogenetic analysis provided important insights about the presence of ribosomal variants in Glomus, with potential negative implication in phylogeny and species recognition.

Entamoeba histolytica, throughout its lifecycle, encounters a variety of stressful conditions. This parasite possesses Heat Shock Response Elements (HSEs) which are crucial for regulating the ex-pression of various genes, aiding in its adaptation and survival. These HSEs are regulated by Heat Shock Transcription Factors (EhHSTFs). Our research has identified seven such factors in this parasite, designated as EhHSTF1 through EhHSTF7. Significantly, under heat shock condi-tions and in the presence of the antiamoebic compound emetine, EhHSTF5, EhHSTF6, and EhHSTF7 show overexpression, highlighting their essential role in gene response to these stressors. Currently, only EhHSTF7 has been confirmed to recognize the HSE in the promoter of the EhPgp5 gene (HSE_EhPgp5), leaving the binding potential of the other EhHSTFs to HSE yet to be explored. Consequently, our study aimed to examine both in vitro and in silico the oligomeri-zation and binding capabilities of the recombinant EhHSTF5 protein (rEhHSTF5) to HSE_EhPgp5. The in vitro results indicate that the oligomerization of rEhHSTF5 is concentration-dependent, with its dimeric conformation showing a higher affinity for HSE_EhPgp5 than its monomeric state. In silico analysis suggests that the alpha 3 α-helix (α3-helix) of the DNA-binding domain (DBD5) of EhHSTF5 is crucial in binding to the major groove of HSE, primarily through hydro-gen bonding and salt-bridge interactions. In summary, our results highlight the importance of oligomerization in enhancing the affinity of rEhHSTF5 for HSE_EhPgp5 and demonstrate its abil-ity to specifically recognize structural motifs within HSE_EhPgp5. These insights significantly contribute to our understanding of one of the potential molecular mechanisms employed by the parasite to efficiently respond to various stressors, thereby enabling successful adaptation and survival within its host environment.

DNA barcoding has emerged as a powerful tool in the field of taxonomy, transforming the way we identify and classify species. This review article aims to provide an up-to-date overview of the advancements in DNA barcoding techniques, their applications, and their impact on taxonomy and biodiversity studies. We will explore the evolution of DNA barcoding, the development of standardized barcode regions, and the challenges and limitations associated with this methodology. Additionally, we will delve into the diverse range of taxonomic groups for which DNA barcoding has been applied, highlighting key case studies and their contributions to our understanding of biodiversity. Furthermore, we will discuss the integration of DNA barcoding with other molecular and bioinformatic approaches, such as metabarcoding and machine learning, to enhance species identification and biodiversity assessment. This review aims to provide a comprehensive perspective on how DNA barcoding is reshaping the field of taxonomy and its implications for conservation, ecology, and evolutionary biology.

Proteolysis Targeting Chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD) with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focusses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.

Background: The aim was to diagnose Candida in the oral cavity of subjects with type 2 diabetes mellitus (T2DM) using a genotyping technique and to compare the results with those from con-ventional diagnosis by Papanicolau (Pap) staining. Methods: Palatal mucosa smears were per-formed in 18 dental care patients diagnosed with T2DM and grade I, II, and III prosthetic stomatitis who met the inclusion criteria; 18 healthy control subjects were also included in the study. He-moglobin A1c (HbA1c) levels were determined from total blood. Using exfoliative cytology, the Pap staining technique was used to diagnose candidiasis. Exfoliative cytology was also used for molecular diagnosis; DNA was obtained for Candida genotyping and RNA was used for gene ex-pression studies. Results: Clinical patterns indicated that all subjects were positive for Candida; however, Pap analysis revealed only three positive subjects, whereas end-point polymerase chain reaction (PCR) analysis revealed fifteen subjects with some type of Candida. The most common Candida species found were Candida guilliermondii (38.8%), Candida krusei (33.3%), Candida tropicalis, and Candida lusitaniae (22.2%). Interestingly, the coexpression of different species of Candida was found in various patients. In all patients, HbA1c levels were increased. Gene expression analysis showed a significant decrease (p ≤ 0.05) in TLR2 expression in positive subjects, whereas TLR4 expression did not differ significantly among patients. Conclusions: The end-point PCR technique showed better sensitivity for diagnosis of Candida when compared with diagnosis by Pap staining. T2DM subjects showed an increased presence of C. guilliermondii that was correlated with decreased TLR2 expression

The high prevalence of thyroid nodules and increased availability of neck ultrasound have led to an increased incidence of diagnostic thyroid fine needle aspirations, with approximately 20% yielding indeterminate results. The recent availability of molecular tests has helped guide the clinical management of these cases. This paper aims to review and compare three main commercially available molecular cytology platforms in the U.S. – Afirma GSC, Thyroseq GC, and ThyGeNEXT+ThyraMIR. Sequential improvements of the Afirma GSC and Thyroseq GC tests have led to higher positive and negative predictive values, sensitivity, and specificity. Comparative studies revealed similar diagnostic performance between these tests, with considerations for factors such as cost and processing time. Thyroseq GC provides detailed genomic information and specific management recommendations. ThyGeNEXT+ThyraMIR, though less studied, presents promising results, particularly in miRNA analysis for weak driver mutations. Challenges in interpreting results include variations in reporting and the evolving nature of testing platforms. Questions persist regarding cost-effectiveness and the utility of ultrasound characteristics in selecting candidates for molecular testing. While molecular testing has primarily served diagnostic purposes, advancements in understanding genetic alterations now offer therapeutic implications. FDA-approved options target specific genetic alterations, signaling a promising future for tailored treatments.

Coarse-grained molecular dynamics simulations are employed to investigate spatiotemporal evolution of vesicles (polymersomes) via self-assembly of randomly distributed amphiphilic diblock copolymers in water. Vesiculation pathway consists of several intermediate structures such as spherical/rodlike aggregates, wormlike micelles, lamellae, and cavities. Lamella to vesicle transition occurs at a constant aggregation number and is accompanied by a reduction in the solvent accessible surface area. Simulation predictions are in qualitative agreement with the mechanism of vesicle formation in which the unfavorable hydrophobic interactions between water molecules and polymer segments along the edge of the lamella are eliminated at the expense of gaining curvature energy. However, rod-lamella-vesicle transition is accompanied by an increase in copolymer packing density. Hence, the change in the surface area accompanying vesiculation predicted by the simulations is significantly lower than theoretical estimates. Changes in information entropy, quantified by the expectation of the logarithm of the probability distribution function of the segmental stretch parameter s, defined as the difference between the maximum and instantaneous segmental extension, are statistically insignificant along the vesiculation pathway. For rods, lamellae and polymersomes, s follows a log normal distribution. This is explained based on the configurational dynamics of a single diblock chain in water.

BACE1 is involved in the production of beta-amyloid peptides, and inhibiting its activity is a potential therapeutic strategy for managing Alzheimer's disease, as excessive beta-amyloid accumulation is a characteristic feature of the disease.Computational results suggest that hypericin has the potential to act as an inhibitor of BACE1. The Molecular Docking results indicate a high binding affinity between hypericin and BACE1, with a notable binding energy score of -10.3 kcal/mol. Additionally, the formation of various chemical bonds, including hydrogen bonds and hydrophobic bonds, further supports the idea that hypericin may effectively interact with the active site of BACE1. It's important to note that while the in silico Molecular Docking results are promising, further in vitro and in vivo studies would be necessary to validate and better understand the inhibitory potential of hypericin against BACE1. Additionally, the practical application of hypericin as a BACE1 inhibitor in a therapeutic context would require careful consideration of factors such as bioavailability, safety, and efficacy.