Assessment of NIR-triggered PEG-coated NaGdF4:Tm3+/Yb3+bio-compatible upconversion nanoparticles for contrast enhancement in OCT imaging and optical thermometry.

In this investigation, we embarked on the synthesis of polyethylene glycol coated NaGdF4:Tm3+/Yb3+upconversion nanoparticles (UCNPs), aiming to assess their utility in enhancing image contrast within the context of swept source optical coherence tomography (OCT) and photo-thermal OCT imaging. Our research unveiled the remarkable UC emissions stemming from the transitions of Tm3+ions, specifically the1G4→3H6transitions, yielding vibrant blue emissions at 472 nm. We delved further into the UC mechanism, meticulously scrutinizing decay times and the nanoparticles' capacity to convert radiation into heat. Notably, these nanoparticles exhibited an impressive photo-thermal conversion efficiency of 37.5%. Furthermore, our investigations into their bio-compatibility revealed a promising outcome, with more than 90% cell survival after 24 h of incubation with HeLa cells treated with UCNPs. The nanoparticles demonstrated a notable thermal sensitivity of 4.7 × 10-3K-1at 300 K, signifying their potential for precise temperature monitoring at the cellular level.

NaYF4:Ho3+/Yb3+@NaGdF4 core@shell upconversion nanoparticles for contrast enhancement in bimodal in-vitro OCT imaging.

Contrast enhancement is explored in optical coherence tomography images using core NaYF4:Ho3+/Yb3+ and core@shell NaYF4:Ho3+/Yb3+@NaGdF4 nanoparticles. Under 980 nm excitation, core@shell nanoparticles exhibited 2.8 and 3.3 times enhancement at 541 nm and 646 nm emission wavelengths of Ho3+ ions compared to core nanoparticles. Photo-thermal conversion efficiencies were 32% and 20% for core and core@shell nanoparticles. In swept-source optical coherence tomography (SSOCT), core@shell nanoparticles have shown superior contrast, while in photo-thermal optical coherence tomography (PTOCT) core nanoparticles have excelled due to their higher photo-thermal conversion efficiency. The enhancement in contrast to noise ratio obtained is 58 dB. Comparative assessments of scattering coefficients and contrast-to-noise ratios were conducted, providing insights into nanoparticle performance for contrast enhancement in optical coherence tomography.

Edible oil based optical clearing for optical coherence tomography angiography imaging.

In optical imaging, optical clearing agents are commonly used to enhance the structural details of a sample. The current study investigates how to use it to improve the data obtained by an optical coherence tomography angiography system. A natural edible oil with no chemical base has been used for optical clearing. In-vivo testing on mice and humans yielded excellent optical clearing. Using computational techniques, the improvement in angiography signal caused by the optical clearing agent is investigated qualitatively and quantitatively. Compared to the control group, applying the edible oil-based optical clearing agent demonstrated improved vessel percentage and refined vascular signal intensity along depth.

Automatic segmentation of layers in chorio-retinal complex using Graph-based method for ultra-speed 1.7 MHz wide field swept source FDML optical coherence tomography.

The posterior segment of the human eye complex contains two discrete microstructure and vasculature network systems, namely, the retina and choroid. We present a single segmentation framework technique for segmenting the entire layers present in the chorio-retinal complex of the human eye using optical coherence tomography (OCT) images. This automatic program is based on the graph theory method. This single program is capable of segmenting seven layers of the retina and choroid scleral interface. The graph theory was utilized to find the probability matrix and subsequent boundaries of different layers. The program was also implemented to segment angiographic maps of different chorio-retinal layers using "segmentation matrices." The method was tested and successfully validated on OCT images from six normal human eyes as well as eyes with non-exudative age-related macular degeneration (AMD). The thickness of microstructure and microvasculature for different layers located in the chorio-retinal segment of the eye was also generated and compared. A decent efficiency in terms of processing time, sensitivity, and accuracy was observed compared to the manual segmentation and other existing methods. The proposed method automatically segments whole OCT images of chorio-retinal complex with augmented probability maps generation in OCT volume dataset. We have also evaluated the segmentation results using quantitative metrics such as Dice coefficient and Hausdorff distance This method realizes a mean descent Dice similarity coefficient (DSC) value of 0.82 (range, 0.816-0.864) for RPE and CSI layer.

Exploration of molecular interactions between scoparone and associated compounds with Constitutive androstane receptor (CAR) leading to gallstone prevention: an in silico investigation.

Scoparone (6, 7 dimethylesculetin) is a biologically active compound derived from the herb Artemisia capillaris having anti-inflammatory, anti-lipemic, and anti-allergic roles. Activation of the constitutive androstane receptor (CAR) in primary hepatocytes of both wild-type and humanized CAR mice by scoparone, accelerates bilirubin and cholesterol clearance in vivo. This can prevent gallstones which is a dreaded gastrointestinal disease. To date, surgery is regarded as the gold standard for treating gallstones. The molecular interactions between scoparone and CAR leading to gallstone prevention are not yet explored. In this study, we have analyzed these interactions through an insilico approach. After extracting the CAR structures (mice and human) from the protein databank and 6, 7-dimethylesuletin from PubChem, energy minimization of both the receptors was done to make them stable followed by docking. Next, a simulation was performed to stabilize the docked complexes. Through docking, H-bonds and pi-pi interactions were found in the complexes, which imply a stable interaction, thus activating the CAR. A similarity search for scoparone was performed and the selected compounds were docked with the CAR receptors. Esculentin acetate and scopoletin acetate interacted with human CAR through pi-alkyl and H-bond respectively. While Fraxidin methyl ether, fraxinol methyl ether, and 6, 7 diethoxycoumarin interacted with mice CAR through H-bond and Pi-Pi T-shaped bonds. The selected complexes were simulated further. Our results are in accordance with the hypothesis in the literature. We have also analyzed the drug likeliness, absorption, non-carcinogenicity, and other properties of scoparone which can support further in vivo studies.Communicated by Ramaswamy H. Sarma.

Exploring the impact of PVC and PVA microplastics on zebrafish tissue using multi-spectral imaging, Optical Coherence Tomography (OCT) and biospeckle OCT (bOCT).

Plastics are widely used in industry and households, but improper disposal has caused their accumulation in aquatic systems worldwide. As a result, mechanical and photochemical processes break down these plastics into microplastics or nano plastics, posing a severe threat to marine organisms and humans as they enter the food chain. This study investigates the effect of Polyvinyl chloride (PVC) and Polyvinyl alcohol (PVA) microplastics in zebrafish by using multi-spectral imaging (MSI), Optical Coherence Tomography (OCT), and Biospeckle OCT (bOCT). These techniques allow for long-term studies in the fish without invasive procedures in real-time. Zebrafish were exposed to Nile red labeled PVC and PVA for 21 days with 500mg/L concentration. Image acquisition and analysis were performed every five days till the end of the study. MSI images revealed deposition of microplastics in the gills region of the fish; some diffused deposition was seen throughout the body in the PVA group towards the end of the experiment. The effect of these MPs on the structure of the gills and their exact location was determined by capturing OCT images. bOCT was used to determine the average speckle contrast for all the OCT images to determine the change in biological activity within the gills region. An increase in bioscpeckle contrast was observed for the MPs treated groups compared to the control group. PVC appeared to cause a more considerable rise in activity compared to PVA. The results indicated that the MPs exert stress on the gills and increase activity within the gills, possibly due to the blockage of the gills and disruption of the water filtration process, which could be monitored non-invasively only by using bOCT. Overall, our study demonstrates the usefulness of non-invasive, robust techniques like MSI, bOCT, and biospeckle for long-term zebrafish studies and real-time analyses.

Exploring the Effect of Size Variability on Efficiency of Upconversion Nanoparticles as Optical Contrast Agents.

The current works explores the optical contrast property and nanaotheranostic capabilities of the rare earth based Upconversion nanoparticles. Optical coherence tomography (OCT) has been used to explore the particles ability to increase contrast and improve signal intensity. Photo thermal OCT, a function extension of OCT has been used to gauge the photo thermal potential of the nanoparticles. The nanoparticles successfully improved contrast and information from the deeper layers of the sample. The particles also showed excellent capability for use as photo thermal agents.

In vivo morphological study of obese development in mice model guided by swept-source optical coherence tomography (SSOCT).

This article shows the adequacy of the custom-built optical imaging system in the advancement investigation of obese mice. Obesity is defined as increased adipose/fatty mass resulting from a chronic imbalance between energy intake and expenditure. The in vivo investigation was performed for the tissue characterization of obese mice utilizing swept-source optical coherence tomography (SSOCT) for in situ examination and histology of delicate tissues in mice skin. It provides a noninvasive, painless visualization of the subsurface in life systems. Our SSOCT system's data is comparable to the regular invasive histology. Cross-assessment is done in various skin layers in obese mice like epidermis, papillary dermis, dermis, and fat tissue, which are likewise separated from the nonobese mice group. Histopathology results were further assessed with the obtained SSOCT results. This high precision of characterizing tissues using SSOCT helps us perform in vivo imaging and can also be used for the variable purpose of clinical practice.

A computational analysis of molecular evolution for virulence genes of zoonotic novel coronavirus (COVID-19).

Zoonotic Novel coronavirus disease 2019 (COVID-19) is highly pathogenic and transmissible considered as emerging pandemic disease. The virus belongs from a large virus Coronaviridae family affect respiratory tract of animal and human likely originated from bat and homology to SARA-CoV and MERS-CoV. The virus consists of single-stranded positive genomic RNA coated by nucleocapsid protein. The rate of mutation in any virulence gene may influence the phenomenon of host radiation. We have studied the molecular evolution of selected virulence genes (HA, N, RdRP and S) of novel COVID-19. We used a site-specific comparison of synonymous (silent) and non-synonymous (amino acid altering) nucleotide substitutions. Maximum Likelihood genealogies based on differential gamma distribution rates were used for the analysis of null and alternate hypothesis. The null hypothesis was found more suitable for the analysis using Likelihood Ratio Test (LRT) method, confirming higher rate of substitution. The analysis revealed that RdRP gene had the fastest rate evolution followed by HA gene. We have also reported the new motifs for different virulence genes, which are further useful to design new detection and diagnosis kit for COVID -19.

Study of lipase producing gene in wheat - an in silico approach.

BACKGROUND: Lipases (EC 3.1.1.3) catalyze the hydrolysis of oil into free fatty acids and glycerol forming the 3rd largest group of commercialized enzymes. Plant lipases grab attention recently because of their specificity, less production and purified cost, and easy availability. In silico approach is the first step to identify different genes coding for lipase in a most common indigenous plant, wheat, to explore the possibility of this plant as an alternative source for commercial lipase production. As the hierarchy organization of genes reflects an ancient process of gene duplication and divergence, many of the theoretical and analytical tools of the phylogenetic systematics can be utilized for comparative genomic studies. Also, in addition to experimental identification and characterization of genes, for computational genomic analysis, Arabidopsis has become a popular strategy to identify crop genes which are economically important, as Arabidopsis genes had been well identified and characterized for lipase. A number of articles had been reported in which genes of wheat have shown strong homology with Arabidopsis. The complete genome sequences of rice and Arabidopsis constitute a valuable resource for comparative genome analysis as they are representatives of the two major evolutionary lineages within the angiosperms. Here, in this in silico approach, Arabidopsis and Oryza sativa serve as models for dicotyledonous and monocotyledonous species, respectively, and the genomic sequence data available was used to identify the lipase genes in wheat. RESULTS: In this present study, Ensembl Plants database was explored for lipase producing gene present in wheat genome and 21 genes were screened down as they contain specific domain and motif for lipase (GXSXG). According to the evolutionary analysis, it was found that the gene TraesCS5B02G157100, located in 5B chromosome, has 58.35% sequence similarity with the reported lipase gene of Arabidopsis thaliana and gene TraesCS3A02G463500 located in the 3A chromosome has 51.74% sequence similarity with the reported lipase gene of Oryza sativa. Homology modeling was performed using protein sequences coded by aforementioned genes and optimized by molecular dynamic simulations. Further with the help of molecular docking of modeled structures with tributyrin, binding efficiency was checked, and the difference in energies (DE) was -9.83 kcal/mol and -6.67 kcal/mol, respectively. CONCLUSIONS: The present work provides a basic understanding of the gene-encoding lipase in wheat, which could be easily accessible and used as a potent industrial enzyme. The study enlightens another direction which can be used further to explore plant lipases.

Polymerically engineered upconversion nanoparticles (UCNPs) as contrast agent for functionally modified optical coherence tomography (OCT).

Upconversion nanoparticles (UCNPs) are widely recognized exogenous contrast agents for bioimaging. Swept source optical coherence tomography (SSOCT) is a non-invasive imaging tool commissioned for cross-sectional imaging of the biological sample. We present polymerically modified UCNPs as a potential contrast agent for SSOCT. In this communication, functionalized NaYF4: Ho3+/Yb3+ UCNPs were synthesized for more bioavailability with a coating of two different polymers namely, polyethylene glycol (PEG) and polyvinylpyrrolidone (PVP). Time-dependent diffusion dynamics of functionalized UCNPs were performed in-vivo with a mice model. Imaging was performed with both inactive and excited UCNPs. A separate optical system was developed with an amplitude modulated 980 nm laser source to excite UCNPs. UCNPs with PVP coating shows better results compared to others in terms of increase of scattering coefficients and contrast-to-noise ratio. The complete system is designed with purpose to enhance imaging contrast of tissue at molecular level with further possible extension as a theranostics system for tumor imaging during photodynamic therapy.

Albumin-PEG-Based Biomaterial for Laser-Tissue Soldering and Its Real-Time Monitoring With Swept-Source Optical Coherence Tomography.

BACKGROUND AND OBJECTIVES: The study presents a noninvasive, real-time monitoring technique for the cross-sectional imaging of the laser-tissue soldering process with a swept-source optical coherence tomography (SSOCT) system. The study also aims at performing a comparative study of the laser-tissue soldering (LTS) process using optimized compositions of albumin as solder biomaterials. STUDY DESIGN/MATERIALS AND METHODS: The experimental study was conducted both ex vivo and in vivo to assess the superiority of the LTS process over conventional methods using a noninvasive imaging tool. In our attempt to combine the two techniques into one diagnostic tool, we have used the SSOCT system for a thoroughgoing investigation of the process in real-time. Laser-assisted tissue soldering was performed using a pulsed near-infrared (NIR) laser with a central wavelength of 980 nm, an output power of 5 W, and beam diameter (1/e 2 ) of 6 mm. Here, the SSOCT system has been utilized to observe and analyze the transitions taking place in real-time without disrupting the process. For the comparative study, we have used serum albumin in a 70% w/v concentration and albumin-PEG conjugate in a 6:1 ratio as soldering materials. Different stages of the laser interaction process were monitored with OCT B-scans of the incision area. Also, the basis of biomaterial-tissue interaction was studied with the help of Fourier-transform infrared spectroscopy (FTIR) analysis of the soldering materials. RESULTS: FTIR spectrum alludes to the fact that the intertwining of the soldering biomaterial with tissue collagen creates adhesion. Biomaterial serum albumin with 70% w/v concentration as soldering material demonstrates complete sealing of tissue at the incision with 3 minutes of laser irradiation. SSOCT B-scans have been useful in imaging the incision noninvasively at different stages. CONCLUSION: Both ex vivo and in vivo demonstration of the LTS process were presented with a clinical resemblance. OCT can be of great value to determine the wound contraction in case of incisional wounds or sealed wounds produced by the LTS procedure. Also, volumetric measurements of percentage reduction in wound area can be done with OCT. SSOCT system can be a potential imaging modality for real-time noninvasive imaging of surgical procedures like LTS. Lasers Surg. Med. © 2021 Wiley Periodicals LLC.

Investigation of Gd2O3: Er3+/Yb3+ Upconversion Nanoparticles (UCNPs) as a Multi-model Contrast Agent for Functional Optical Coherence Tomography (fOCT).

Currently, upconversion nanoparticles (UCNPs) implanted as a contrast agent for optical coherence tomography (OCT) system due to its biocompatibility, anti-stock emission, narrow emission bandwidth non-photobleaching effects etc., but it was not used as multi model imaging probe. We synthesized multimodal imaging probe having upconversion property along with paramagnetic property and used as dual contrast agents for Photothermal Optical Coherence Tomography (PTOCT) and Magnetomotive Optical Coherence Tomography (MMOCT). The synthesized Gd2O3:Er3+/Yb3+ UCNPs shows the bright yellow upconversion emission, biocompatibility with hydrophilic property. A custom built SSOCT setup modified for PTOCT and MMOCT imaging along with custom MATLAB algorithm for signal extraction. A dynamic study was performed with synthesized UCNPs as an imaging probe and functional OCT system for targeted imaging. This shows the utility of the Gd2O3:Er3+/Yb3+ UCNPs as molecular probe for targeted imaging applications.

Computational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy.

Nitrilase enzyme (a green catalyst) is an industrially important enzyme which hydrolyses various nitrile compounds (containing -CN functional group) into amides and corresponding carboxylic acids. The current study explored the binding affinity and a method to enhance the catalysis activity of the enzyme using computational approaches. Four mutants were generated using sequential site-directed mutagenesis aiming that an increase in hydrogen bonds that will further increase binding efficiency towards the ligand. Molecular dynamics simulation was rigorously performed to check the stability of those mutants followed by docking to verify its interaction with the ligand. Various statistical dynamics analyses were performed to validate the structure. All the studies predict that built mutants are stable. Mutants 2 and 3 showed a better affinity towards acrylamide by forming the highest number of hydrogen bonds implying better catalysis. The binding affinity values of the Mutant 2 and Mutant 3 with acrylamide are -7.44 kcal/mol and -7.17 kcal/mol, respectively. This study may prove useful for the industry to develop efficient nitrilase enzymes with improved catalytic activity.Communicated by Ramaswamy H. Sarma.

Ex-vivo molecular imaging with upconversion nanoparticles (UCNPs) using photo thermal optical coherence tomography (PTOCT).

We demonstrate a photothermal optical coherence tomography (PTOCT) system, with upconversion nanoparticles (UCNPs) as a molecular probe. We synthesized hydrophilic, biocompatible upconversion nanoparticles (UCNPs) using hydrothermal synthesis. We developed the PTOCT system along with the signal processing tool and applied this technique on animal tissue phantom for targeted imaging. The 'lock-in detection' of the amplitude modulated photothermal beam (980 nm), which used to excite the UCNPs was the backbone of the signal processing algorithm. The signal processing was further established in different aspects. As an application part, the diffusion dynamics of the UCNPs was performed inside the tissue to study molecular movement and subsequent changes in tissue properties. A comparison of photothermal optical coherence tomography (PTOCT) with phase variance optical coherence tomography (PVOCT) for targeted molecular imaging also presented.

Real-time assessment and characterization of immobilized lipase onto a natural matrix and qualitative reaction kinetic studies using swept-source optical coherence tomography.

The current study presents a method based on Optical Coherence Tomography (OCT) for non-destructive, real-time analysis and portrayal of immobilization efficacy for lipase on a natural matrix namely, eggshell. Subsequently, qualitative biochemical reaction kinetics of immobilized lipase was also studied. Successful immobilization of lipase on eggshell was confirmed by the presence of a clear peak in 'A' scan of OCT image. From immobilization kinetics it is clearly observed that the thickness of the highest peak of the A-scan increases significantly and peak intensity saturated after 90 min of incubation. Hydrolysis of oil using immobilized lipase indicated that the release of free fatty acids increased up to 8 h during reaction and the result was in accordance with the 'B' scan data of the OCT system. Changes in scattering coefficient-based analysis were performed with respect to incubation time to showcase the immobilization process and hydrolysis reaction of lipase. Scanning electron microscope analysis with smoother surface indicated presence of lipase on eggshell matrices, with no further change after oil hydrolysis.

In silico pharmacophore modeling and simulation studies for searching potent antileishmanials targeted against Leishmania donovani nicotinamidase.

Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD+) in the subsequent steps. Leishmania protozoan parasites are NAD+ auxotrophs and need precursors (nicotinamide, nicotinic acid, nicotinamide riboside) from their host environment to synthesize NAD+ for their survival. Interestingly, absence of this enzyme in higher eukaryotes and its absolute requirement in the developmental cycle of Leishmania has led nicotinamidase an attractive drug target towards leishmaniasis. Hence, we report some potential inhibitors for nicotinamidase screened based on 3-D pharmacophore model consisting of "ML", "Hyd|Aro", "Acc" and "Excl vol" features. Subsequently, dynamics simulation studies validate the proposed pharmacophore model suggesting its reliability for future studies. Furthermore, these essential site-specific features will help in enhancing the inhibition of nicotinamidase activity. Results of our study suggest that blocking of active site of nicotinamidase by the identified lead inhibitor will have major impact on the infectious processes and the survival of the parasite. Furthermore, due to the structural homology in the enzyme among L. donovani, L. infantum, L. major, we anticipate that our study would help to design more potent drug candidates against leshmaniasis for these three species.

Engineering of Gadolinium-Decorated Graphene Oxide Nanosheets for Multimodal Bioimaging and Drug Delivery.

Engineering of water-dispersible Gd3+ ions-decorated reduced graphene oxide (Gd-rGO) nanosheets (NSs) has been performed. The multifunctional capability of the sample was studied as a novel contrast agent for swept source optical coherence tomography and magnetic resonance imaging, and also as an efficient drug-delivery nanovehicle. The synthesized samples were fabricated in a chemically stable condition, and efforts have been put toward improving its biocompatibility by functionalizing with carbohydrates molecules. Gd incorporation in rGO matrix enhanced the fluorouracil (5-FU) drug loading capacity by 34%. The release of the drug was ∼92% within 72 h. Gd-rGO nanosheets showed significant contrast in comparison to optically responsive bare GO for swept source optical coherence tomography. The longitudinal relaxivity rate (r 1) of 16.85 mM-1 s-1 for Gd-rGO was recorded, which was 4 times larger than that of the commercially used clinical contrast agent Magnevist (4 mM-1 s-1) at a magnetic field strength of 1.5 T.

A comparative multivariate analysis of nitrilase enzymes: An ensemble based computational approach.

Nitrilases, member of nitrilase superfamily catalyse the hydrolysis of different nitriles to corresponding amides and acids. In this article, we demonstrate two-fold computational comparative analysis on coding gene sequences, amino acid sequences, three-dimensional structure of the nitrilases from different species and discovered conserved motifs linked with related species. A large ensemble-based dataset was utilized from bacteria, fungi, plants and animals. Here, we used comparative genomics, motif analyses and Bayesian phylogenetic analyses in combination with structural analyses [molecular dynamics simulation, principal component analysis (PCA), dynamic cross correlation (DCCM), root mean squared inner product (RMSIP), free energy surface (FES)] to investigate the evolution, ecological relationship and structure-function association of nitrilase family. The inferred evolutionary tree displayed nitrilase gene clusters to be shared among bacteria, fungi and plants. Structural analysis revealed that the folding of catalytic sites is similar among species; however, the loop region varies. We provide evidence based on PCA that the nitrilases are clustered into different clades due to variation in side chains. Numerous of significant correlations were found between sequence clades and the structural discriminating properties of nitrilases originating from different species. The results are consistent with the hypothesis that bacterial nitrilases are in ecological and evolutionary relationships with fungi and plants during plant-pathogen interaction to large extent. This compact and detail results also open new dimensions for further studying and improvement of industrially important nitrilase enzymes.

Mutational analysis of phenolic acid decarboxylase from Enterobacter sp. Px6-4. towards enhancement of binding affinity: A computational approach.

Microbial Ferulic Acid Decarboxylase (FADase) catalyses the conversion of ferulic acid to 4-hydroxy-3-methoxystyrene (4-vinylguaiacol) via non-oxidative decarboxylation. In this article, we present a computational, three-dimensional structural and functional analysis of FADase from Enterobacter sp. P × 6-4 (3NX1) which can be used to generate enhanced bindings of substrates. The enzymatic catalytic site and binding sites have been critically evaluated. Sequential site directed mutations on enzyme have also been introduced for formation of a greater number of hydrogen bonds. Four mutants were generated based on our hypothesis. Active sites of mutated FADases have been analyzed with dynamic cross-correlation maps and principle components analysis. All structures were validated and optimized through energy minimization. Docking studies were also carried out between ferulic acid and different mutated enzymes. The protein (wild and mutants) complexes were further validated with molecular simulation. Mutant3 was found to have better affinity towards ferulic acid. Mutant3 also forms a higher number of hydrogen bonds with the substrate to facilitate greater interaction. This current work will help industry to create new and novel mutants to produce vanillin.