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Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of toehold-mediated strand displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by 'leakage'-the spurious activation of the reaction leading to high background signals and false positives. Here, we introduce the Y-Switch, a new TMSD cascade design that recognizes a custom nucleic acid input and generates an amplified output. The Y-Switch is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Y-Switches detect native RNA under isothermal conditions without reverse transcription or pre-amplification, with a detection threshold as low as â¼200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.
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Preservatives are critical ingredients in various pharmaceutical and consumer products. In particular, a high efficacy preservative system is essential in enhancing the shelf-life and safety of these products. However, the development of such a preservative system heavily relies on experimental approaches. In this study, molecular dynamics (MD) simulation was complemented with quantitative structure-activity relationship (QSAR) modelling to comprehensively evaluate polymer-preservative interactions between three different polymers (polyethylene terephthalate, PET; polypropylene, PP; and cellulose) and a series of preservatives from the classes of aliphatic, aromatic, and organic acids. First, adsorption of preservatives onto polymer surfaces was simulated in an aqueous environment. The preservatives did not adhere to hydrophilic cellulose, but most preservatives were adsorbed by PET and PP in distinct configurations. Interaction energies (IEs) between the preservatives and the polymers generally increase from cellulose to PP and PET. The diffusion coefficients of preservatives are dependent on polymer nature, preservative structure, and their resulting molecular interactions. Linear and low molecular weight preservatives exhibit higher diffusion coefficients in polymers. For a particular preservative, diffusion coefficients increased in the order of cellulose < PET < PP. Finally, using MD properties and molecular descriptors of preservatives, QSAR models were developed to identify key descriptors of preservatives and predict their IEs and diffusion coefficients in polymers. This study demonstrates a computational approach for identifying critical materials properties, and predicting polymer-preservative molecular interactions in water. Such an approach streamlines the rational selection and design of high efficacy preservative systems for various pharmaceutical, food and cosmetic products. Furthermore, the integrated computational strategy also reduces trial-and-error experimental efforts, thereby accelerating the development of high efficacy preservative systems.
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Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of -4.1, -3.2, and -3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of -27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.Communicated by Ramaswamy H. Sarma.
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The Transcription factor II B (TFIIB)related factor 2 (BRF2) containing TFIIIB complex recruits RNA polymerase III multi-subunit complex to selective gene promoters that altogether are responsible for synthesizing a variety of small non-coding RNAs, including a special type of selenocysteine tRNA (tRNASec), micro-RNA (miRNA), and other regulatory RNAs. BRF2 has been identified as a potential oncogene that promotes cancer cell survival under oxidative stress through its genetic activation. The structure of the BRF2 protein was modeled using the Robetta server, refined, and validated using the Ramachandran plot. A virtual approach utilizing molecular docking was used to screen a natural compound library to determine potential compounds that can interact with the molecular pin motif of the BRF2 protein using Maestro (Schrodinger). Subsequent molecular dynamics simulation studies of the top four ligands that exhibited low glide scores were performed using GROMACS. The findings derived from the simulations, in conjunction with the exploration of hydrogen bonding patterns, evaluation of the free energy landscape, and thorough analysis of residue decomposition, collectively converged to emphasize the robust interaction characteristics exhibited by Ligand 366 (Deacetyl lanatoside C) and ligand 336 (Neogitogenin)-with the BRF2 protein. These natural compounds may be potential inhibitors of BRF2, which could modulate the regulation of selenoprotein synthesis in cancer cells. Targeting BRF2 using these promising compounds may offer a new therapeutic approach to sensitize cancer cells to ferroptosis and apoptosis.Communicated by Ramaswamy H. Sarma.
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Three-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.
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Células Madre Mesenquimatosas , Organoides , Animales , Perros , Humanos , Hidrogeles , ADN , MamíferosRESUMEN
Stereoselective syntheses of pyrrolidines and piperidines bearing hydrophobic chains have been achieved through a metal free, Lewis acid-mediated 5/6-endo-dig reductive hydroamination cascade of enynyl amines. The brevity of the developed strategy allowed for the collective stereoselective total synthesis of various alkaloids, including (±)-pyrrolidine cis-225H, (±)-epi-197B, (±)-epi-225C, the family of (+)-solenopsins and (+)-isosolenopsins, and the formal synthesis of (±)-bgugaine and (+)-azimic acid.
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The final stage of almost all chronic kidney diseases is renal fibrosis. Simple wounds or persistent inflammation can cause tissue inflammation, which, in the case of the kidney, results in scarring. Vascular sclerosis, tubulointerstitial fibrosis and glomerular fibrosis are all types of kidney fibrosis. Renal damage and fibrosis are caused by elevated expression of CXCR4. This study aimed to identify possible pharmacological agents which could bind to and inhibit isoform I of CXCR4 and determine their strength of interactions. The I-TASSER, Galaxyweb and Robetta were used to predict and refine the structure of the CXCR4 protein. ModBase was used to improve the loops, and then the quality was evaluated by using the ERRAT value (92.15) and Ramachandran plot. The improved 3D structure was subjected to small molecule database docking using Maestro (from Schrodinger) and the glide module. GROMACS was used to simulate molecules with the three top low glide scores and the best ADME properties. The best glide score was achieved by ligand ID 4990 (-11.5). Simulations, free energy landscape and residue decomposition analysis revealed that 4990 interacted more consistently with CXCR4 than the other two small molecules.Communicated by Ramaswamy H. Sarma.
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Regioselective amination of polyhalogenated heteroarenes (especially pyrimidines) has extensive synthetic and commercial relevance for drug synthesis applications but is plagued by the lack of effective synthetic strategies. Herein, we report the Cu(II)/PTABS-promoted highly regioselective nucleophilic aromatic substitution (SNAr) of polychlorinated pyrimidines assisted by DFT predictions of the bond dissociation energies of different C-Cl bonds. The unique reactivity of Cu(II)-PTABS has been attributed to the coordination/activation mechanism that has been known to operate in these reactions, but further insights into the catalytic species have also been provided.
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As a sequel to our recent study on the oxidation by O2, i. e., autoxidation of dissolved hydrogen sulfide, H2S, in aqueous medium, we present here the results of a similar study in rain water medium. The rainwater sampling was done sequentially for four years (2016-2019). In all 67 samples of rainwater were collected on event basis during monsoon period (June-October) in and around the Campus of University of Rajasthan, Jaipur (26°50Ì N-75°52Ì E), which is situated in a semi-arid region adjacent to the Thar Desert in the North-Western part of the India having an annual average rainfall of 54 cm. ICP-MS technique was used in the analysis of rainwater and more than 30 metals were detected, which included transition metals, rare earths, less common metals. Beryllium, vanadium, silver, selenium, manganese, cerium, gallium, yttrium, barium, cesium, copper, rubidium, arsenic, lanthanum, cadmium, lead, uranium and bismuth were common to all rain water samples.H2S oxidation by dissolved oxygen was studied in rainwater as well as in laboratory water media for comparison. The kinetics rate law was: -d[O2]/dt = k1K1[H+][S][O2]t/( [H+]2 + K1[H+] + K1K2), where K1 is first dissociation constant of H2S and k1 is the rate constant for the dominant reaction step:HS- + O2 â products.
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Sulfuro de Hidrógeno , Metales Pesados , Sulfuro de Hidrógeno/análisis , Oxígeno/análisis , Cinética , Monitoreo del Ambiente , Plata/análisis , Lluvia , Agua/análisis , Metales Pesados/análisisRESUMEN
Solid dispersion of poorly soluble APIs is known to be a promising strategy to improve dissolution and oral bioavailability. To facilitate the development and commercialization of a successful solid dispersion formulation, understanding of intermolecular interactions between APIs and polymeric carriers is essential. In this work, first, we assessed the molecular interactions between various delayed-release APIs and polymeric excipients using molecular dynamics (MD) simulations, and then we formulated API solid dispersions using a hot melt extrusion (HME) technique. To assess the potential API-polymer pairs, three quantities were evaluated: (a) interaction energy between API and polymer [electrostatic (Ecoul), Lenard-Jones (ELJ), and total (Etotal)], (b) energy ratio (API-polymer/API-API), and (c) hydrogen bonding between API and polymer. The Etotal quantities corresponding to the best pairs: NPX-Eudragit L100, NaDLO-HPMC(P), DMF-HPMC(AS) and OPZ-HPMC(AS) were -143.38, -348.04, -110.42, and -269.43 kJ/mol, respectively. Using a HME experimental technique, few API-polymer pairs were successfully extruded. These extruded solid forms did not release APIs in a simulated gastric fluid (SGF) pH 1.2 environment but released them in a simulated intestinal fluid (SIF) pH 6.8 environment. The study demonstrates the compatibility between APIs and excipients, and finally suggests a potential polymeric excipient for each delayed-release API, which could facilitate the development of the solid dispersion of poorly soluble APIs for dissolution and bioavailability enhancement.
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Fusarium oxysporum f. sp. Lycopersici (FOL) is a soilborne pathogen that infects tomato plants and inflicts severe damage, resulting in heavy yield losses worldwide, causing Fusarium wilt disease. FOL encodes several pathogenicity factors necessary for colonizing and invading the host plants. Secreted in Xylem (SIX), a pathogenicity factor, is a small cysteine-rich fungal protein found in the xylem sap of FOL-infected tomato plants, which plays a major role in determining host specificity and in contributing to pathogenicity/virulence. However, the structure of SIX1 has not been modeled yet. Therefore, this study aimed to elucidate the structure of SIX1 by comparative modeling using Robetta server. The best possible structures obtained were then refined, validated, and utilized for subsequent analysis. An antifungal library comprising 16,824 compounds was screened to determine small molecules that can interact with SIX1. Five antifungal compounds were identified from the library. Further analyses revealed that, of the five ligands, 4-[(2-(3-methoxyphenoxy)acetyl)amino] benzamide exhibited the capacity to stably interact with SIX1. This shows that 4-[[2-(3-methoxyphenoxy)acetyl]amino] benzamide can be used as a potential candidate in the prevention of FOL infection. In summary, small-molecule inhibitors such as 4-[[2-(3-methoxyphenoxy)acetyl]amino] benzamide could be highly effective in combating FOL infection, along with biocontrol methods and strategies that use transgenic plants overexpressing resistance genes.
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Vibrio cholerae causes cholera, an acute diarrhoeal disease. The virulence in V. cholerae is regulated by the quorum-sensing mechanism and response regulator LuxO positively regulates the expression of virulence determinants adhesion, biofilm formation, and cholera toxin production. Previous in-silico studies revealed that 2-methoxy-4-vinylphenol could bind to the ATP binding site of LuxO and the complex was compact and stable in pHs like intestinal pHs. Here, we have explored the polymeric nano-formulation of 2-methoxy-4-vinylphenol using cellulose acetate phthalate for controlled drug release and their effectiveness in attenuating the expression of V. cholerae virulence. Physico-chemical characterization of the formulation showed particles with a mean size of 91.8 ± 14 nm diameter and surface charge of - 14.7 ± 0.07 mV. The uniform round polymeric nanoparticles formed displayed about 51% burst release of the drug at pH 7 by 3rd h, followed by a controlled linear release in alkaline pH. The polymeric nanoparticles demonstrated a tenfold increase in intestinal membrane permeability ex-vivo. At lower concentrations, the 2-methoxy-4-vinylphenol polymeric nanoparticles were non-cytotoxic to Int 407 cells. In-vitro analysis at pH 6, pH 7, pH 8, and pH 9 revealed that cellulose acetate phthalate-2-methoxy-4-vinylphenol nanoparticles were non-bactericidal at concentrations up to 500 µg/mL. At 31.25 µg/mL, the nanoparticles inhibited about 50% of the biofilm formation of V. cholerae MTCC 3905 and HYR14 strains. At this concentration, the adherence of V. cholerae MTCC 3905 and HYR14 to Int 407 cell lines were also significantly affected. Gene expression analysis revealed that the expression of tcp, qrr, and ct at pH 6, 7, 8, and 9 has reduced. The CAP-2M4VP nanoparticles have demonstrated the potential to effectively reduce the virulence of V. cholerae in-vitro.
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Cólera , Polímeros de Estímulo Receptivo , Vibrio cholerae , Humanos , Vibrio cholerae/genética , Proteínas Bacterianas/metabolismo , Compuestos de Vinilo/metabolismo , Regulación Bacteriana de la Expresión GénicaRESUMEN
Encapsulation into nanoparticles (NPs) is a potential method to deliver pharmaceutical/cosmetic actives deep into the skin. However, understanding the NP formulations and underlying mechanism of active delivery to skin has scarcely been studied. We report a simulation platform that screens, evaluates, formulates, and provides atomic-resolution interpretation of NP-based formulations, and reveals the active permeation mechanism from NPs to skin. First, three actives, namely, ferulic acid (FA), clotrimazole (CZE), and tretinoin (TTN), and five lipid excipients' (Compritol, Precirol, Geleol, Gelot, Gelucire) combinations were screened by MD simulations for the best pairs. For each suggested pair, the actual active and lipid compositions for the synthesis of stable NP formulations were then obtained by experiments. MD simulations demonstrate that in NP formulations, FA and CZE actives are present at the surface of the NPs, whereas TTN actives are present at both the surface and interior of the NP core. The NP shapes obtained by simulation perfectly match with experiments. For each NP, separate MD simulations illustrate that active-loaded NPs approach the skin surface quickly, and then actives translocate from NP surface to skin surface followed by penetration of NPs through skin. The driving force for the translocation which initiates during the penetration process, is the stronger active-skin interaction compared to active-NP interaction. Permeation free energy indicates spontaneous transfer of actives from solution phase to the surface of the skin bilayer. The free energy barriers are increased in the order of FA < TTN < CZE. Significantly lower diffusions of actives are obtained in the main barrier region compared to bulk, and the average diffusion coefficients of actives are in the same order of magnitude (â¼10-6 cm2/s). The estimated permeability coefficients (log P) of actives are mainly governed by free energy barriers. The study would facilitate the development of novel lipid-based NP formulations for personal-care/pharmaceutical applications.
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Simulación de Dinámica Molecular , Nanopartículas , Piel , Liposomas , LípidosRESUMEN
Introduction: Refractive error is the inability of eyes to focus clearly on images. Visual impairment due to refractive error has a major impact on children's education and daily activities. The hospital has no documentation of the ocular morbidity related to refractive errors in children. The aim of this study was to find out the prevalence of refractive error in children visiting the Department of Paediatric Ophthalmology of a tertiary care centre. Methods: A descriptive cross-sectional study was done in the Outpatient Department of Paediatric Ophthalmology in a tertiary care centre from 8 September 2022 to 7 March 2023 after obtaining ethical approval from the Institutional Review Committee. A convenience sampling method was used. The point estimate was calculated at 95% Confidence Interval. Results: Among 3600 children, the prevalence of refractive error was seen in 668 children (18.56%) (15.61-21.51, 95% Confidence Interval). Refractive error was seen in 363 (54.34%) boys and 305 (45.66%) girls. Myopia was found in 340 (50.90%), astigmatism in 207 (30.99%), and hyperopia in 121 (18.11%). Conclusions: The prevalence of refractive error among children attending a tertiary care centre was found to be higher than studies done in similar settings. Regular screening of refractive error for visual impairment is recommended among school going children. Keywords: astigmatism; hyperopia; myopia; refractive error; visual impairment.
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Astigmatismo , Hiperopía , Miopía , Errores de Refracción , Masculino , Femenino , Niño , Humanos , Astigmatismo/epidemiología , Hiperopía/epidemiología , Centros de Atención Terciaria , Estudios Transversales , Agudeza Visual , Errores de Refracción/epidemiología , Errores de Refracción/diagnóstico , Miopía/epidemiología , Prevalencia , Trastornos de la Visión/epidemiologíaRESUMEN
TMSOTf-mediated reaction of alkynyl vinylogous carbonates serendipitously gave 1,4-oxazepine and dihydropyran dienes via transposition of an ethyl acrylate moiety involving intramolecular cascade Prins-type cyclization/retro-oxa-Michael reaction/cycloisomerisation. The developed atom-economical protocol selectively provides an E double bond geometry. Dihydropyran dienes could be reduced diastereoselectively using Et3SiH/TMSOTf or could be transformed into polycyclic heterocycles by Heck reaction.
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INTRODUCTION: Retinitis Pigmentosa (RP) is a group of diffuse retinal degenerative diseases predominantly affecting the rod and cone photoreceptors. The prevalence of retinitis pigmentosa seen in literature is approximately 1:4000. Retinitis Pigmentosa is one of the the most common causes of blindness in the age group of 20 to 40 years. The objective of this study was to determine the profile of retinitis pigmentosa in Terai and Nepal-India border region considering patients seeking care at a Tertiary level Eye Hospital in the terai region (southern part) of Nepal. MATERIALS AND METHODS: A hospital-based, retrospective study was carried out at R. M. Kedia Eye Hospital. A total of 385 (83 males and 107 females from Nepal and 109 males and 86 females from India) diagnosed patients of Retinitis Pigmentosa were included in the study. Data was collected over a period of eleven years from 2008-2018. RESULTS: Out of 385 diagnosed Retinitis Pigmentosa patients, 192 (49.87%) were male and 193 (50.13%) were female with slightly female predominance. The prevalence of RP seen in our study was 0.03%. About 51% of the patients visited here were from India and nearby border areas/ villages which cover most of the rural areas of India. In this study it was found that 49.34% of the RP cases were from Nepal, of which 43.63% of cases were from Hindu community and 5.71% from Muslim community and about 50.66% cases of RP were from India, of which 37.67% from Hindu and 12.98% from Muslim community. The peak age of presentation of RP was at 30-39 years (29.09%), followed by 20-29 years (26.75%). The common marriage pattern of consanguinity was found in Muslim community in between the first cousins. In this study the hospital record did not show any evaluation for the syndromic disease in the hospital record, though RP is usually non syndromic and there are literatures where many syndromic forms have been identified. CONCLUSION: The prevalence of RP seen in the study was 0.03% (A total of 1101299 sample population of which 385 patients had RP). Since RP is an inherited disease and is one of the non-treatable causes of blindness which runs in the families, a role of counseling to reduce consanguineous marriages should be brought forward to reduce the disease process.
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Enfermedades de la Retina , Retinitis Pigmentosa , Adulto , Ceguera/epidemiología , Ceguera/etiología , Femenino , Hospitales , Humanos , Masculino , Nepal/epidemiología , Prevalencia , Retinitis Pigmentosa/diagnóstico , Retinitis Pigmentosa/epidemiología , Estudios Retrospectivos , Adulto JovenRESUMEN
Aluminum is a widely popular material due to its low cost, low weight, good formability and capability to be machined easily. When a non-metal such as ceramic is added to aluminum alloy, it forms a composite. Metal Matrix Composites (MMCs) are emerging as alternatives to conventional metals due to their ability to withstand heavy load, excellent resistance to corrosion and wear, and comparatively high hardness and toughness. Aluminum Matrix Composites (AMCs), the most popular category in MMCs, have innumerable applications in various fields such as scientific research, structural, automobile, marine, aerospace, domestic and construction. Their attractive properties such as high strength-to-weight ratio, high hardness, high impact strength and superior tribological behavior enable them to be used in automobile components, aviation structures and parts of ships. Thus, in this research work an attempt has been made to fabricate Aluminum Alloys and Aluminum Matrix Composites (AMCs) using the popular synthesis technique called stir casting and join them by friction stir welding (FSW). Dissimilar grades of aluminum alloy, i.e., Al 6061 and Al 1100, are used for the experimental work. Alumina and Silicon Carbide are used as reinforcement with the aluminum matrix. Mechanical and corrosion properties are experimentally evaluated. The FSW process is analyzed by experimentally comparing the welded alloys and welded composites. Finally, the best suitable FSW combination is selected with the help of a Multi-Attribute Decision Making (MADM)-based numerical optimization technique called Weighted Aggregated Sum Product Assessment (WASPAS).
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INTRODUCTION: The outbreak of coronavirus disease in Nepal led medical colleges to suspend in person teaching-learning activities and ultimately online platform was introduced to deliver the contents of medical education. The objective of this study was to describe the perception of medical students towards online teaching-learning introduced during the COVID-19 outbreak in Nepal. METHODS: An online survey using a descriptive cross-sectional study design was carried out among 515 undergraduate medical students currently enrolled in medical colleges in Nepal. Ethical approval was sought from Nepal Health Research Council to conduct this study, and digital informed consent was taken from study respondents. A semi-structured questionnaire in Google form was utilized to collect data. The link of the Google form was sent to the potential respondents through email and social media. Descriptive statistics, including frequency, percentage, mean, and standard deviation were used to analyze data in Stastical Package for the Social Sciences version 20. Ethical approval was sought from Nepal Health Research Council to conduct this study, and digital informed consent was taken from study respondants. RESULTS: The overall score of perception of online teaching-learning was 17.61±7.19, which indicated many problems in this method of teaching-learning. The mean score of perception of online teaching-learning was found to be different across sex, location of enrolled medical colleges, having a personal electronic device, having an internet connection at residence, having separate room/space for attending online classes, and self-rated computer skills. Moreover, only 28 (5.4%) of respondents had perceived online teaching-learning as a better method of delivering content of medical curricula. CONCLUSIONS: Surveyed medical students in Nepal were found to perceive many problems in online teaching-learning. Moreover, management and faculty members need to take the necessary measures for enhancing the online teaching-learning quality.