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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.

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 (r1) 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.

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.

Graphical abstract, 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.

In-vitro imaging by swept-source optical coherence tomography (OCT) represents a class of advanced tomography that provides comprehensive and accurate clinical diagnostics. Here colloidal NaGdF4:Er3+/Yb3+ particles having an average size of 32 nm were successfully synthesized by a facial thermal decomposition method and then used as a contrast agent in OCT imaging. Prepared phosphor has shown bright green upconversion emission under 976 nm diode laser. The phosphor particles had increased the scattering of OCT scanning radiation, and thus higher image contrast was observed. The results indicate that upconversion phosphors may work as suitable contrast agents for OCT imaging.

Improving the industrial enzyme for better yield of the product is important and a challenging task. One of such important industrial enzymes is microbial Hydroxycinnamoyl-CoA hydratase-lyase (HCHL). It converts feruloyl-CoA to vanillin. We place our efforts towards the improvement of its catalytic activity with comprehensive computational investigation. Catalytic core of the HCHL was explored with molecular modeling and docking approaches. Site-directed mutations were introduced in the catalytic site of HCHL in a sequential manner to generate different mutants of HCHL. Basis of mutation is to increase the interaction between HCHL and substrate feruloyl-CoA through interatomic forces and hydrogen bond formation. A rigorous molecular dynamics (MD) simulation was performed to check the stability of mutant’s structure. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), dynamic cross correlation (DCCM) and principal component analysis (PCA) were also performed to analyze flexibility and stability of structures. Docking studies were carried out between different mutants of HCHL and feruloyl-CoA. Investigation of the different binding sites and the interactions with mutant HCHLs and substrate allowed us to highlight the improved performance of mutants than wild type HCHL. This was further validated with MD simulation of complex consisting of different mutants and substrate. It further confirms all the structures are stable. However, mutant-2 showed better affinity towards substrate by forming hydrogen bond between active site and feruloyl-CoA. We propose that increase in hydrogen bond formation might facilitate in dissociation of vanillin from feruloyl-CoA. The current work may be useful for the future development of ‘tailor-made’ enzymes for better yield of vanillin.

Optical Coherence Tomography (OCT) and angiography is widely considered as a significant achievement for non-invasive bio-medical imaging which have also been used for visualization of microstructure and microvasculature of tissue, noninvasively. This makes use of class of algorithmic technique which fall under the domain of optical coherence tomography angiography (OCTA), which includes the use of mainly phase variance, Doppler, and speckle variance. Despite some inherent advantages, many of these algorithms, namely phase variance and speckle variance suffer from certain drawbacks, which necessitates post-processing of the generated image, thereby incurring a chance for the loss of information. In this article, we propose an alternative iterative technique based on amplitude variance subtraction, which can be used in an independent manner to visualize the blood vessels. Results shown are comparable in their nature with existing phase variance and speckle variance methods but without the requirement of any additional filters or post-processing and is also free from the erroneous phase jumps and phase stabilization.

Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and translational selection. Lower GC12 and higher GC3S in all three parasites suggests that the ancestral highly expressed genes (HEGs), compared to lowly expressed genes (LEGs), might have been rich in AT-content. This also suggests that there must have been a faster rate of evolution under GC-bias in LEGs. It was observed from the estimation of synonymous/non-synonymous substitutions in HEGs that the HEG dataset of L. donovani is much closer to L. major evolutionarily. This is also supported by the higher dN value as compared to dS between L. donovani and L. major, suggesting the conservation of synonymous codon positions between these two species and the role of translational selection in shaping the composition of protein-coding genes.

Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bioinformatics tools. Multivariate analysis has been used as a tool to study codon bias perspectives of xylanases. It was further observed that the codon usage of xylanases genes from different fungal sources is not similar and to reveal this phenomenon the relative synonymous codon usage (RSCU) and base composition variation in fungal xylanase genes were also studied. The codon biasing data like GC content at third position (GC(3S)), effective codon number (N(C)), codon adaptive index (CAI) were further analyzed with statistical softwares like Sigma1plot 9.0 and Systat 11.0. Furthermore, study of translation selection was also performed to verify the influences of codon usage variation among the 94 xylanase genes. In the present study xylanase gene from 12 organisms were analyzed and codon usages of all xylanases from each organism were compared separately. Analysis indicates biased codon among all 12 fungi taken for study with Aspergillus nidulans, Chaetomium globosum, Aspergillus terreus and Aspergillus clavatus showing maximum biasing. N(C) plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in fungal xylanase gene. To reveal the relative synonymous codon usage and base composition variation in xylanase, 94 genes from 12 fungi were used as model system.

Halo blight disease caused due Pseudomonas syringae results extensive losses in dry Beans. Phage therapy can be tried as an alternative treatment. For evaluation of synonymous codon usage and codon variation, 20 phages of Pseudomonas has been taken for testing. The effect of GC concentration in the phages can be considered for analyzing virulence in these phages. Mutational biasing and translational selection are also the important factors for predicting the appropriate biasing, which can be analyzed through Nc plot and correspondence analysis. Our analysis indicating that out of 20 phages 3 phages namely phage D3, D3112 and 119X are extremely virulent as they have high translational efficiency. Based on our data, we conclude that the phage D3 will be best suited as a phage therapy for treatment against halo blight disease.

Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.

The phenomenon of host radiation is strongly influenced by the rates of mutation of their virulence genes. We have studied the molecular evolution of virulence genes (HA, NS, PB2) of the Avian Influenza Virus H5N1 from avian to human hosts. We used a site-specific comparison of synonymous (silent) and non-synonymous (amino acid altering) nucleotide substitutions for the three chosen genes in parasite populations from different hosts. Analyses were made using Maximum Likelihood (ML) genealogies for the null and alternate hypothesis based on differential gamma distribution rates. The null hypothesis had a higher rate of substitution and was found to be more suitable for all the studied genes by Likelihood Ratio Test (LRT). The study showed the NS gene to be having the fastest rate of evolution.

We demonstrate a noninvasive, three-dimensional, depth-resolved imaging of stratified media with a swept source optical coherence tomography (SS-OCT) system at 1064 nm centre wavelength. A swept source laser is used to enable imaging rate of 100 kHz (100,000 A-scans/s). A comparison between SS-OCT and other imaging modalities is also presented. Brief theory, detail instrumentation of the system and signal processing method are described. The system has axial and transverse resolution of 5 and 14 μm in air respectively. The potential and performance of the system was tested, and two- and three-dimensional imaging of different objects like human skin, infrared detection card, leaf, etc. has been presented.

Light-based diagnostic techniques provide a minimally invasive way for selective biomarker estimation when tissues transform from a normal to a malignant state. Spectroscopic techniques based on diffuse reflectance characterize the changes in tissue hemoglobin/oxygenation levels during the tissue transformation process. Recent clinical investigations have shown that changes in tissue oxygenation and microcirculation are observed in diabetic subjects in the initial and progressive stages. In this pilot study, we discuss the potential of diffuse reflectance spectroscopy (DRS) in the visible (Vis) range to differentiate the skin microcirculatory hemoglobin levels between normal and advanced diabetic subjects with and without neuropathy. Average concentration of hemoglobin as well as hemoglobin oxygen saturation within the probed tissue volume is estimated for a total of four different sites in the foot sole. The results indicate a statistically significant decrease in average total hemoglobin and increase in hemoglobin oxygen saturation levels for diabetic foot compared with a normal foot. The present study demonstrates the ability of reflectance spectroscopy in the Vis range to determine and differentiate the changes in tissue hemoglobin and hemoglobin oxygen saturation levels in normal and diabetic subjects. � 2015 Springer Science+Business Media New York.

We demonstrate the feasibility of our newly developed phase stabilized high-speed (100 kHz A-scans/s) 1 μm sweptsource optical coherence tomography (SSOCT) system with the phase-variance based motion contrast method for visualization of human chorioretinal complex microcirculation. Compared to our previously reported spectral domain (spectrometer based) phase-variance (pv)-SDOCT system it has advantages of higher sensitivity, reduced fringe washout for high blood flow speeds and deeper penetration in choroid. High phase stability SSOCT imaging was achieved by using a computationally efficient phase stabilization approach. This process does not require additional calibration hardware and complex numerical procedures. Our phase stabilization method is simple and can be employed in a variety of SS-OCT systems. Examples of vasculature in the chorioretinal complex imaged by pv-SSOCT is presented and compared to retinal images of the same volunteers acquired with fluorescein angiography (FA) and indocyanine green angiography (ICGA).

Optical coherence tomography is used to demonstrate the modes of a semiconductor laser used in supermarkets. The experiment is low cost and can be adopted for an undergraduate or graduate physics laboratory. The results enable students to understand the voltage-current and optical power characteristics of a semiconductor laser, and provide insight into the nature of radiation below and above the lasing regions.

© OSA 2014. We illustrate a high-speed (100 kHz) high penetration phase stabilized swept source optical coherence angiography (SSOCA) system for in vivo volumetric depth-resolved vasculature imaging of anterior and posterior segment of human eye.

Publisher’s Note: Three-dimensional anterior segment imaging in patients with type 1 Boston Keratoprosthesis with switchable full depth range swept source optical coherence tomography Raju Poddar Dennis E. Cortes John S. Werner Mark J. Mannis Robert J. Zawadzki Downloaded From: http://biomedicaloptics.spiedigitallibrary.org/ on 02/10/2016 Terms of Use: http://spiedigitallibrary.org/ss/TermsOfUse.aspx

A high-speed (100 kHz A-scans/s) complex conjugate resolved 1 μ swept source optical coherence tomography (SS-OCT) system using coherence revival of the light source is suitable for dense three-dimensional (3-D) imaging of the anterior segment. The short acquisition time helps to minimize the influence of motion artifacts. The extended depth range of the SS-OCT system allows topographic analysis of clinically relevant images of the entire depth of the anterior segment of the eye. Patients with the type 1 Boston Keratoprosthesis (KPro) require evaluation of the full anterior segment depth. Current commercially available OCT systems are not suitable for this application due to limited acquisition speed, resolution, and axial imaging range. Moreover, most commonly used research grade and some clinical OCT systems implement a commercially available SS (Axsun) that offers only 3.7 mm imaging range (in air) in its standard configuration. We describe implementation of a common swept laser with built-in k-clock to allow phase stable imaging in both low range and high range, 3.7 and 11.5 mm in air, respectively, without the need to build an external MZI k-clock. As a result, 3-D morphology of the KPro position with respect to the surrounding tissue could be investigated in vivo both at high resolution and with large depth range to achieve noninvasive and precise evaluation of success of the surgical procedure. © The Authors.

© The Authors. We present a noninvasive phase-variance (pv)-based motion contrast method for depth-resolved imaging of the human chorioretinal complex microcirculation with a newly developed phase-stabilized high speed (100-kHz A-scans/s) 1-μm swept-source optical coherence tomography (SSOCT) system. Compared to our previous spectral-domain (spectrometer based) pv-spectral domain OCT (SDOCT) system, this system has the advantages of higher sensitivity, reduced fringe wash-out for high blood flow speeds and deeper penetration in choroid. High phase stability SSOCT imaging was achieved by using a computationally efficient phase stabilization approach. This process does not require additional calibration hardware and complex numerical procedures. Our phase stabilization method is simple and can be employed in a variety of SSOCT systems. Examples of vasculature in the chorioretinal complex imaged by pv-SSOCT from normal as well as diseased eyes are presented and compared to retinal images of the same subjects acquired with fluorescein angiography and indocyanine green angiography. Observations of morphology of vascular perfusion in chorioretinal complex visualized by our method are listed.