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.

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.

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.

Synthesis of NaYF4:Ho3+/Yb3+ colloidal upconversion phosphor and its application for OCT-based imaging, temperature sensing, fingerprinting and security ink

In this work, an NaYF4:Ho3+/Yb3+ upconversion phosphor in colloidal form was synthesized and then its suitability for image contrast enhancement in optical coherence tomography (OCT) and photothermal (PT) OCT imaging was analysed.

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.

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.

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.

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.

Challenges and advantages in wide-field optical coherence tomography angiography imaging of the human retinal and choroidal vasculature at 1.7-MHz A-scan rate

We present noninvasive, three-dimensional, depth-resolved imaging of human retinal and choroidal blood circulation with a swept-source optical coherence tomography (OCT) system at 1065-nm center wavelength. Motion contrast OCT imaging was performed with the phase-variance OCT angiography method. A Fourier-domain mode-locked light source was used to enable an imaging rate of 1.7 MHz. We experimentally demonstrate the challenges and advantages of wide-field OCT angiography (OCTA). In the discussion, we consider acquisition time, scanning area, scanning density, and their influence on visualization of selected features of the retinal and choroidal vascular networks. The OCTA imaging was performed with a field of view of 16 deg (5  mm×5  mm) and 30 deg (9  mm×9  mm). Data were presented in en face projections generated from single volumes and in en face projection mosaics generated from up to 4 datasets. OCTA imaging at 1.7 MHz A-scan rate was compared with results obtained from a commercial OCTA instrument and with conventional ophthalmic diagnostic methods: fundus photography, fluorescein, and indocyanine green angiography. Comparison of images obtained from all methods is demonstrated using the same eye of a healthy volunteer. For example, imaging of retinal pathology is presented in three cases of advanced age-related macular degeneration.

Mutational analysis of microbial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) towards enhancement of binding affinity: A computational approach

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.

Homology model, molecular dynamics simulation and novel pyrazole analogs design of Candida albicans CYP450 lanosterol 14 α-demethylase, a target enzyme for antifungal therapy

Candida albicans infections and their resistance to clinically approved azole drugs are major concerns for human. The azole antifungal drugs inhibit the ergosterol synthesis by targeting lanosterol 14α-demethylase of cytochrome P450 family. The lack of high-resolution structural information of fungal pathogens has been a barrier for the design of modified azole drugs. Thus, a preliminary theoretical molecular dynamic study is carried out to develop and validate a simple homologous model using crystallographic structure of the lanosterol 14α-demethylase of Mycobacterium tuberculosis (PDB ID-1EA1) in which the active site residues are substituted with that of C. albicans (taxid 5476). Further, novel designed pyrazole analogs (SGS1-16) docked on chimeric 1EA1 and revealed that SGS-16 show good binding affinity through non-bonding interaction with the heme, which is different from the leading azole antifungals. The ADME-T results showed these analogs can be further explored in design of more safe and effective antifungal agents.

De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection

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.

In vivo volumetric depth-resolved vasculature imaging of human limbus and sclera with 1μm swept source phase-variance optical coherence angiography

We present nnnnnin vivo volumetric depth-resolved vasculature images of the anterior segment of the human eye acquired with phase-variance based motion contrast using a high-speed (100 kHz, 10⁵ A-scans/s) swept source optical coherence tomography system (SSOCT). High phase stability SSOCT imaging was achieved by using a computationally efficient phase stabilization approach. The human corneo-scleral junction and sclera were imaged with swept source phase-variance optical coherence angiography and compared with slit lamp images from the same eyes of normal subjects. Different features of the rich vascular system in the conjunctiva and episclera were visualized and described. This system can be used as a potential tool for ophthalmological research to determine changes in the outflow system, which may be helpful for identification of abnormalities that lead to glaucoma.

In vivo imaging of human vasculature in the chorioretinal complex using phase-variance contrast method with phase-stabilized 1-μm swept-source optical coherence tomography

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- ource 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.

Characterization and functional analysis of eugenol O-methyltransferase gene reveal metabolite shifts, chemotype specific differential expression and developmental regulation in Ocimum tenuiflorum L

Eugenol-O-methyltransferase (EOMT) catalyzes the conversion of eugenol to methyleugenol in one of the final steps of phenylpropanoid pathway. There are no comprehensive reports on comparative EOMT gene expression and developmental stage specific accumulation of phenylpropenes in Ocimum tenuiflorum. Seven chemotypes, rich in eugenol and methyleugenol, were selected by assessment of volatile metabolites through multivariate data analysis. Isoeugenol accumulated in higher levels during juvenile stage (36.86 ng g(-1)), but reduced sharply during preflowering (8.04 ng g(-1)), flowering (2.29 ng g(-1)) and postflowering stages (0.17 ng g(-1)), whereas methyleugenol content gradually increased from juvenile (12.25 ng g(-1)) up to preflowering (16.35 ng g(-1)) and then decreased at flowering (7.13 ng g(-1)) and post flowering (5.95 ng g(-1)) from fresh tissue. Extreme variations of free intracellular and alkali hydrolysable cell wall released phenylpropanoid compounds were observed at different developmental stages. Analyses of EOMT genomic and cDNA sequences revealed a 843 bp open reading frame and the presence of a 90 bp intron. The translated proteins had eight catalytic domains, the major two being dimerisation superfamily and methyltransferase_2 superfamily. A validated 3D structure of EOMT protein was also determined. The chemotype Ot7 had a reduced reading frame that lacked both dimerisation domains and one of the two protein-kinase-phosphorylation sites; this was also reflected in reduced accumulation of methyleugenol compared to other chemotypes. EOMT transcripts showed enhanced expression in juvenile stage that increased further during preflowering but decreased at flowering and further at postflowering. The expression patterns may possibly be compared and correlated to the amounts of eugenol/isoeugenol and methyleugenol in different developmental stages of all chemotypes.

Three-dimensional anterior segment imaging in patients with type 1 Boston Keratoprosthesis with switchable full depth range swept source optical coherence tomography

A high-speed (100 kHz A-scans/s) complex conjugate resolved 1 μm 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.

Intranuclear matrix metalloproteinases promote DNA damage and apoptosis induced by oxygen-glucose deprivation in neurons

Degradation of the extracellular matrix by elevated matrix metalloproteinase (MMP) activity following ischemia/reperfusion is implicated in blood-brain barrier disruption and neuronal death. In contrast to their characterized extracellular roles, we previously reported that elevated intranuclear MMP-2 and -9 (gelatinase) activity degrades nuclear DNA repair proteins and promotes accumulation of oxidative DNA damage in neurons in rat brain at 3-h reperfusion after ischemic stroke. Here, we report that treatment with a broad-spectrum MMP inhibitor significantly reduced neuronal apoptosis in rat ischemic hemispheres at 48-h reperfusion after a 90-min middle cerebral artery occlusion (MCAO). Since extracellular gelatinases in brain tissue are known to be neurotoxic during acute stroke, the contribution of intranuclear MMP-2 and -9 activities in neurons to neuronal apoptosis has been unclear. To confirm and extend our in vivo observations, oxygen-glucose deprivation (OGD), an in vitro model of ischemia/reperfusion, was employed. Primary cortical neurons were subjected to 2-h OGD with reoxygenation. Increased intranuclear gelatinase activity was detected immediately after reoxygenation onset and was maximal at 24h, while extracellular gelatinase levels remained unchanged. We detected elevated levels of both MMP-2 and -9 in neuronal nuclear extracts and gelatinase activity in neurons co-localized primarily with MMP-2. We found a marked decrease in PARP1, XRCC1, and OGG1, and decreased PARP1 activity. Pretreatment of neurons with selective MMP-2/9 inhibitor II significantly decreased gelatinase activity and downregulation of DNA repair enzymes, decreased accumulation of oxidative DNA damage, and promoted neuronal survival after OGD. Our results confirm the nuclear localization of gelatinases and their nuclear substrates observed in an animal stroke model, further supporting a novel role for intranuclear gelatinase activity in an intrinsic apoptotic pathway in neurons during acute stroke injury.

Study of codon bias perspective of fungal xylanase gene by multivariate analysis

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.

Modifications of ampicillin structure and its implication: an in-silico approach

Structural modifications of the existing ampicillin are much needed for saving patients from ampicillin-resistant microorganisms. A number of new molecules were generated by side chain modification of the existing ampicillin structure. Armed with molecular docking softwares like FlexiDOC, GLIDE, and AutoDOCK, a docking study was performed. Interaction between new molecules and target protein (1W2N) was also executed. Finally, we arranged new molecules according to docking scores, which directly reflects the binding affinity to the receptor protein.

Altered claudin expression is a feature of chronic plaque psoriasis

Epithelial tight junctions play a central role in cell-cell adhesion and are necessary for the selective paracellular movement of ions. Claudins are key components of tight junctions and their expression is altered in gut epithelia in a variety of inflammatory enteropathies, including ulcerative colitis and Crohn's disease. Psoriasis is a chronic inflammatory skin disease affecting approximately 2% of the western population, with significantly increased occurrence in individuals with Crohn's disease. Initial studies investigated the expression of claudins in skin of healthy volunteers and patients with chronic plaque psoriasis. We report here that claudins-1 and -3 are the major protein species present in the epidermis of healthy skin; they are expressed on the surface of epidermal keratinocytes, consistent with their localization to tight junctions. In plaques of psoriasis, claudin-1 was not identifiable in the epidermis, although typical staining patterns were observed in clinically normal, uninvolved skin of patients with psoriasis. Claudin-3 was present in the epidermal granular cell layer in normal skin, but was only identified within the cytosol of epidermal keratinocytes in both involved and uninvolved skin of psoriasis patients. We examined further whether exposure of keratinocytes in vitro to pro-inflammatory cytokines mimicked the observed changes in claudin expression seen in chronic plaque psoriasis; lipopolysaccharide, interferon-gamma and tumour necrosis factor-alpha had no effect on claudin protein expression or distribution. Addition of interleukin-1beta, however, resulted in down-regulation of claudins-1 and -3. Tumour necrosis factor-alpha and interleukin-1beta were further used in an in vivo model of skin inflammation; interleukin-1beta alone modulated claudin protein expression in this system. These data demonstrate that epidermal claudin expression is altered in chronic plaque psoriasis and that expression is in part modulated by interleukin-1beta.

Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis

To reveal the relative synonymous codon usage and base composition variation in bacteriophages, six mycobacteriophages were used as a model system here and both parameters in these phages and their host bacteria, Mycobacterium tuberculosis, have been determined and compared. As expected for GC-rich genomes, there are predominantly G and C ending codons in all 6 phages. Both N_{c} plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in the 6 phages. Further analysis indicates that among 6 Mycobacterium phages Che9c, Bxz1 and TM4 may be extremely virulent in nature as most of their genes have high translation efficiency. Based on our data we suggest that the genes of above three phages are expressed rapidly by host's translation machinery. The information might be used to select the extremely virulent Mycobacterium tuberculosis phages suitable for phage therapy.

Adaptive molecular evolution of virulence genes of avian influenza - A virus subtype H5N1: An analysis of host radiation

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.

Functional analysis of B144/LST1: a gene in the tumor necrosis factor cluster that induces formation of long filopodia in eukaryotic cells

B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia differing from those seen on transfection of a dominant active CDC42 gene. The structures are dynamically rearranging and sometimes connect one cell with another. The full effect of B144/LST1 protein on cell morphology requires the retention of at least one of the four cysteines of the peptide plus the presence of a hydrophobic segment in the protein, but requires only one of the two coding regions present in the terminal 3' exons.

Homocysteine induces expression and secretion of monocyte chemoattractant protein-1 and interleukin-8 in human aortic endothelial cells: implications for vascular disease

BACKGROUND

Proinflammatory cytokines play key roles in atherogenesis and disease progression. Because hyperhomocysteinemia is an independent risk factor for cardiovascular disease, we hypothesized that homocysteine could be atherogenic by altering the expression of specific cytokines in vascular endothelial cells.

METHODS AND RESULTS

Northern blot and RNase protection assays showed that DL-homocysteine induced mRNA expression of the proinflammatory cytokines monocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8) in cultured human aortic endothelial cells (HAECs). Homocysteine had no effect on expression of other cytokines, namely tumor necrosis factor-alpha, granulocyte-macrophage colony-stimulating factor, interleukin-1beta, and transforming growth factor-beta. MCP-1 mRNA expression increased 1 hour after homocysteine treatment, reached a maximum within 2 to 4 hours, and declined to basal levels over the next 24 hours. Induction of mRNA expression for both chemokines was observed with as little as 10 micromol/L DL-homocysteine, and maximal expression was achieved with 50 micromol/L DL-homocysteine. Homocysteine also triggered the release of MCP-1 and IL-8 protein from HAECs into the culture medium. The induction was specific for homocysteine, because equimolar concentrations of L-homocystine, L-cysteine, and L-methionine had no effect on mRNA levels and protein release. Furthermore, L-homocysteine induced chemokine expression, but D-homocysteine did not, thus demonstrating enantiomeric specificity. The culture medium from homocysteine-treated HAECs promoted chemotaxis in human peripheral blood monocytes and U937 cells. Anti-human recombinant MCP-1 antibody blocked the migration.

CONCLUSIONS

Pathophysiological levels of L-homocysteine alter endothelial cell function by upregulating MCP-1 and IL-8 expression and secretion. This suggests that L-homocysteine may contribute to the initiation and progression of vascular disease by promoting leukocyte recruitment.

Homocysteine metabolism in cardiovascular cells and tissues: implications for hyperhomocysteinemia and cardiovascular disease

We have determined the activity and protein levels of CBS in a number of cardiovascular cells and tissues by direct enzyme assay and Western blot analysis, respectively. We have also determined the activity of BHMT in these same tissues and cells and have come to the conclusion that neither enzyme is expressed. This results suggests that in the human cardiovascular system homocysteine metabolism is limited to the remethylation pathway catalyzed by MS. Thus, hyperhomocysteinemia in conjunction with a limited metabolic capacity for homocysteine in the cardiovascular system could result in cellular dysfunction.

Role of thyroid hormone in the morphological differentiation and maturation of astrocytes: temporal correlation with synthesis and organization of actin

Morphological changes and the molecular mechanisms associated with the maturation of astrocytes were studied under normal and thyroid hormone-deficient conditions using long-term (30 days) primary cultures derived from the neonatal rat brain. Immunocytochemical staining of cells with a monoclonal antibody specific to glial fibrillary acidic protein demonstrated for the first time that, similar to their maturation in vivo, astrocytes maintained in normal serum-containing medium can undergo complete maturation involving two distinct stages of morphological differentiation (from radial glia to flat polygonal cells with epithelioid morphology and then to mature process-bearing cells with stellate morphology). Deficiency of thyroid hormone delays the first step and totally blocks the second stage of differentiation in the maturation process. Comparative staining of normal and thyroid hormone-deficient astrocytes with filamentous actin-specific fluorescein isothiocyanate-phalloidin and quantitation of the various forms of intracellular actin using an improved DNase I assay demonstrated that maturation of astroglial cells is associated with characteristic alterations in the level of cytoskeletal and noncytoskeletal filamentous (F) actin. In particular, the maintenance of the epithelioid form of the hypothyroid astrocytes is associated with a progressive increase in the level of cytoskeletal F-actin and a concomitant decline in the level of non-cytoskeletal F-actin. Quantitation of actin mRNA by Northern blot analysis and studies on the rate of actin synthesis at various stages of differentiation showed that the initial transformation into the epithelioid form is associated with an increase in the rate of synthesis of actin and the expression of its mRNA, while the final transformation into the nature process-bearing form is correlated with a decline in these parameters. The results indicates that thyroid hormone plays an obligatory role in promoting the differentiation and maturation of astrocytes, and that during this process the hormone regulates the expression of actin and its intracellular organization in a way conducive to morphological differentiation.

Regulation of actin and tubulin gene expression by thyroid hormone during rat brain development

In the developing brain the active neurite outgrowth during the early phase of synaptogenesis is associated with a thyroid hormone dependent expression of tubulin and actin. In this study, the molecular mechanism of thyroid hormone (TH) action on actin and tubulin gene expression in the developing rat brain has been investigated by comparing the steady state levels of both mRNAs with their respective rates of transcription in cerebra from normal and hypothyroid animals. The developmental profile of actin as well as tubulin mRNAs in both normal and hypothyroid brains display a biphasic pattern, increasing progressively during the first week after birth and declining thereafter. However, hypothyroidism resulted in a significant reduction in the steady state levels of both mRNAs during the first postnatal week. During the second and third weeks, in contrast to their rapid decline in the normal controls, the corresponding decrease in the hypothyroid cerebra was retarded and prolonged resulting in their higher levels under TH-deficient condition. Kinetics of stimulation of actin and tubulin mRNAs in the 5-day hypothyroid cerebra following injection of the optimal dose of TH (200 micrograms T3/100 g body wt.) demonstrated elevation of both mRNAs within 1 h indicating a possible role of TH at the transcriptional level. In vitro transcription experiments by nuclear run off assay unambiguously confirmed that actin gene transcription is depressed in the hypothyroid cerebra compared to normal control. This reduced rate of transcription could be significantly induced in the hypothyroid cerebra by incubation of hypothyroid nuclei with T3 prior to transcription. In contrast, except for a reduced transcription in 5-day hypothyroid nuclei, no effect on tubulin gene transcription was evident at any other age. Moreover preincubation of hypothyroid nuclei from all three ages with T3 had no stimulatory effect on tubulin gene transcription. Analysis of age related changes in the rates of transcription of actin and tubulin genes with their corresponding steady state mRNA levels in normal and hypothyroid developing brain provides strong evidence that although additional modes of regulation may be operative, transcription represents an important level of control for thyroidal regulation of actin gene expression while tubulin gene expression is primarily regulated at post-transcriptional level.

A monoclonal antibody to a cytoskeletal protein selectively recognizing malignant neuroectodermal tumors

Fusion of myeloma (P3X63-Ag 8.653) cells with spleen cells from BALB/c mice immunized with human neuroblastoma (SK-N-SH) cells yielded a hybridoma clone, referred to as 3XB7, with a unique pattern of reactivity to malignant neuroectodermal tumors except gliomas of low-grade malignancy. Indirect immunofluorescence staining under different conditions and Western blot analysis indicate that the 3XB7 MAb recognizes an intracellular cytoskeletal protein of M(r) 52K. Immunohistochemical studies with cryostat and paraffin-embedded sections from tumor biopsies revealed that the 3XB7 MAb specifically recognizes malignant neuroectodermal tumors and reacts negatively with other epithelial and mesenchymal tumors, e.g., carcinomas, lymphomas, and sarcomas as well as with normal adult and fetal brain tissues. Negative reaction was also observed with other small round cell tumors of childhood. Thus the 3XB7 antigen can be used for diagnosis of all stages of neuroblastomas, and its specific expression in gliomas with high-grade malignancy (grades III and IV) confer on it additional prognostic value.

Delayed detyrosination of alpha-tubulin from parallel fibre axons and its correlation with impaired synaptogenesis in hypothyroid rat cerebellum

The biochemical basis of retarded differentiation and maturation of microtubules and impaired synaptogenesis in hypothyroidism has been investigated by studying the temporal and spatial relationship between alpha-tubulin detyrosination in the parallel fibre axons of rat cerebellum and alterations in the activity of the detyrosinating enzyme, TTCP (tubulinyl tyrosine carboxypeptidase) with the progress of synaptogenesis in the molecular layer. Detyrosination was monitored by following the disappearance of stain from cerebellar sections, immunocytochemically labeled with a monoclonal antibody (20C6) specific for alpha-tubulin, tyrosinated at the C-terminal end. With respect to normal controls, detyrosination of alpha-tubulin from the parallel fibres of the molecular layer during synaptogenesis was not only delayed by about 5 days but also prolonged in the hypothyroid cerebellum. Correspondingly, the increase of TTCP activity in the developing thyroid deficient cerebellum was also delayed by about 1 week. Comparison of the developmental profile of TTCP activity in the normal and hypothyroid cerebellum during synaptogenesis revealed that the overall activity of the enzyme in the thyroid deficient cerebellum was reduced to almost half of that of the normal controls. These results establish that thyroid hormones are essential for the induction of TTCP, which catalyses detyrosination during the normal ontogenic development of rat cerebellum. Since our data also suggest that detyrosination precedes synaptic contacts to generate a class of differentiated microtubules functionally competent for synaptogenesis, the delayed detyrosination in the hypothyroid cerebellum may desynchronize the normal developmental program resulting in incomplete synaptogenesis.

Incidence and elimination of R plasmids in Vibrio cholerae

Of 124 strains of Vibrio cholerae, 32 were multiply resistant to antibiotics. This resistance appeared to be determined by R plasmids on the basis of their effective elimination by sodium dodecyl sulfate, acridine orange, ethidium bromide, and ultraviolet radiation.