Effects of near-UV radiation on the protein of the grey squirrel lens.

Science.gov (United States)

Zigman, S; Paxhia, T; Waldron, W

1988-06-01

In vivo exposure of grey squirrels to 40W BLB illumination resulted in alterations in the state of the lens crystallins, mainly in the outer layer of the lens. HPLC revealed an increase of the void volume or crosslinked crystallins and an increase in peptides with molecular weights lower than 20,000 d. In vitro exposure of squirrel lens aqueous extracts to Woods lamp radiation (predominantly 365 nm) led to similar but more exaggerated changes as viewed by high performance liquid chromatography. When viewed by polyacrylamide gel electrophoresis (PAGE), soluble protein crosslinking was also observed. The near-UV absorbing chromophores of low molecular weight present in the lens served as photosensitizers that enhanced the protein changes. Sodium azide inhibited the changes, indicating a role for singlet oxygen in the crosslinking.

Effects of near-UV radiation on the protein of the grey squirrel lens

Energy Technology Data Exchange (ETDEWEB)

Zigman, S; Paxhia, T; Waldron, W

1988-06-01

In vivo exposure of grey squirrels to 40W BLB illumination resulted in alterations in the state of the lens crystallins, mainly in the outer layer of the lens. HPLC revealed an increase of the void volume or crosslinked crystallins and an increase in peptides with molecular weights lower than 20,000 d. In vitro exposure of squirrel lens aqueous extracts to Woods lamp radiation (predominantly 365 nm) led to similar but more exaggerated changes as viewed by high performance liquid chromatography. When viewed by polyacrylamide gel electrophoresis (PAGE), soluble protein crosslinking was also observed. The near-UV absorbing chromophores of low molecular weight present in the lens served as photosensitizers that enhanced the protein changes. Sodium azide inhibited the changes, indicating a role for singlet oxygen in the crosslinking.

Adjustable internal structure for reconstructing gradient index profile of crystalline lens.

Science.gov (United States)

Bahrami, Mehdi; Goncharov, Alexander V; Pierscionek, Barbara K

2014-03-01

Employing advanced technologies in studying the crystalline lens of the eye has improved our understanding of the refractive index gradient of the lens. Reconstructing and studying such a complex structure requires models with adaptable internal geometry that can be altered to simulate geometrical and optical changes of the lens with aging. In this Letter, we introduce an optically well-defined, geometrical structure for modeling the gradient refractive index profile of the crystalline lens with the advantage of an adjustable internal structure that is not available with existing models. The refractive index profile assigned to this rotationally symmetric geometry is calculated numerically, yet it is shown that this does not limit the model. The study provides a basis for developing lens models with sophisticated external and internal structures without the need for analytical solutions to calculate refractive index profiles.

Vitreous Humor Changes Expression of Iron-Handling Proteins in Lens Epithelial Cells

Science.gov (United States)

Goralska, Malgorzata; Fleisher, Lloyd N.; McGahan, M. Christine

2017-01-01

Purpose In humans, vitrectomy is associated with development of nuclear cataracts. Iron catalyzes free radical formation causing oxidative damage, which is implicated in cataract formation. This study was designed to determine if vitreous humor, which can initiate differentiation of lens epithelial cells, would have an effect on iron-handling proteins. Methods Cultured canine lens epithelial cells were treated with collected canine vitreous humor. Lysates of treated and control cells were separated by SDS-PAGE. Ferritin H- and L-chains, transferrin receptor 1, and aquaporin 0 were immunodetected and quantitated with specific antibodies. Morphologic changes in treated cells were assessed. Results Treatment of lens epithelial cells with a 33% (vol/vol) solution of vitreous humor changed the morphology of lens cells and induced expression of aquaporin 0, a marker of fiber cell differentiation that was undetectable in control cells. Treatment did not modify the size of iron-handling proteins but significantly increased content of ferritin from 2.9- to 8.8-fold over control and decreased levels of transferrin receptor by 37% to 59%. Conclusions Vitreous humor may significantly limit iron uptake by transferrin/transferrin receptor pathway, and by increasing ferritin levels could profoundly increase the iron-storage capacity of ferritin in lens cells. Vitreous humor may play a significant protective role against iron-catalyzed oxidative damage of lens epithelial cells and therefore in the formation of cataracts. PMID:28245299

The Endocytic Recycling Regulatory Protein EHD1 Is Required for Ocular Lens Development

Science.gov (United States)

Arya, Priyanka; Rainey, Mark A.; Bhattacharyya, Sohinee; Mohapatra, Bhopal; George, Manju; Kuracha, Murali R; Storck, Matthew D.; Band, Vimla; Govindarajan, Venkatesh; Band, Hamid

2015-01-01

The C-terminal Eps15 homology domain-containing (EHD) proteins play a key role in endocytic recycling, a fundamental cellular process that ensures the return of endocytosed membrane components and receptors back to the cell surface. To define the in vivo biological functions of EHD1, we have generated Ehd1 knockout mice and previously reported a requirement of EHD1 for spermatogenesis. Here, we show that approximately 56% of the Ehd1-null mice displayed gross ocular abnormalities, including anophthalmia, aphakia, microphthalmia and congenital cataracts. Histological characterization of ocular abnormalities showed pleiotropic defects that include a smaller or absent lens, persistence of lens stalk and hyaloid vasculature, and deformed optic cups. To test whether these profound ocular defects resulted from the loss of EHD1 in the lens or in non-lenticular tissues, we deleted the Ehd1 gene selectively in the presumptive lens ectoderm using Le-Cre. Conditional Ehd1 deletion in the lens resulted in developmental defects that included thin epithelial layers, small lenses and absence of corneal endothelium. Ehd1 deletion in the lens also resulted in reduced lens epithelial proliferation, survival and expression of junctional proteins E-cadherin and ZO-1. Finally, Le-Cre-mediated deletion of Ehd1 in the lens led to defects in corneal endothelial differentiation. Taken together, these data reveal a unique role for EHD1 in early lens development and suggest a previously unknown link between the endocytic recycling pathway and regulation of key developmental processes including proliferation, differentiation and morphogenesis. PMID:26455409

Characterization of upstream sequences of the LIM2 gene that bind developmentally regulated and lens-specific proteins

Institute of Scientific and Technical Information of China (English)

HSU Heng; Robert L. CHURCH

2004-01-01

During lens development, lens epithelial cells differentiate into fiber cells. To date, four major lens fiber cell intrinsic membrane proteins (MIP) ranging in size from 70 kD to 19 kD have been characterized. The second most abundant lens fiber cell intrinsic membrane protein is MP19. This protein probably is involved with lens cell communication and relates with cataractogenesis. The aim of this research is to characterize upstream sequences of the MP19 (also called LIM2) gene that bind developmentally regulated and lens-specific proteins. We have used the gel mobility assays and corresponding competition experiments to identify and characterize cis elements within approximately 500 bases of LIM2 upstream sequences. Our studies locate the positions of some cis elements, including a "CA" repeat, a methylation Hha I island, an FnuD II site, an Ap1 and an Ap2 consensus sequences, and identify some specific cis elements which relate to lens-specific transcription of LIM2. Our experiments also preliminarily identify trans factors which bind to specific cis elements of the LIM2 promoter and/or regulate transcription of LIM2. We conclude that developmental regulation and coordination of the MP 19 gene in ocular lens fiber cells is controlled by the presence of specific cis elements that bind regulatory trans factors that affect LIM2 gene expression. DNA methylation is one mechanism of controlling LIM2 gene expression during lens development.

UVA photolysis using the protein-bound sensitizers present in human lens

International Nuclear Information System (INIS)

Ortwerth, B.J.; Olesen, P.R.

1994-01-01

This research was undertaken to demonstrate that the protein-bound chromophores in aged human lens can act as sensitizers for protein damage by UVA light. The water-insoluble (WI) proteins from pooled human and bovine lenses were solubilized by sonication in water and illuminated with UV light similar in output to that transmitted by the cornea. Analysis of the irradiated proteins showed a linear decrease in sulfhydryl groups with a 30% loss after 2 h. No loss was seen when native α-crystallin was irradiated under the same conditions. A 25% loss of histidine residues was also observed with the human lens WI fraction, and sodium dodecyl sulfate polyacrylamide gels indicated considerable protein cross-linking. Similar photodamage was seen with a WI fraction from old bovine lenses. While the data show the presence of UVA sensitizers, some histidine destruction and protein cross-linking were also obtained with α-crystallin and with lysozyme which argue that part of the histidine loss in the human WISS was likely due to tryptophan acting as a sensitizer. (Author)

Radiocarbon dating of the human eye lens crystallines reveal proteins without carbon turnover throughout life

DEFF Research Database (Denmark)

Lynnerup, Niels; Kjeldsen, Henrik; Heegaard, Steffen

2008-01-01

, there is no subsequent remodelling of these fibers, nor removal of degraded lens fibers. Human tissue ultimately derives its (14)C content from the atmospheric carbon dioxide. The (14)C content of the lens proteins thus reflects the atmospheric content of (14)C when the lens crystallines were formed. Precise radiocarbon...

Aberration design of zoom lens systems using thick lens modules.

Science.gov (United States)

Zhang, Jinkai; Chen, Xiaobo; Xi, Juntong; Wu, Zhuoqi

2014-12-20

A systematic approach for the aberration design of a zoom lens system using a thick lens module is presented. Each component is treated as a thick lens module at the beginning of the design. A thick lens module refers to a thick lens component with a real lens structure, like lens materials, lens curvatures, lens thicknesses, and lens interval distances. All nine third-order aberrations of a thick lens component are considered during the design. The relationship of component aberrations in different zoom positions can be approximated from the aberration shift. After minimizing the aberrations of the zoom lens system, the nine third-order aberrations of every lens component can be determined. Then the thick lens structure of every lens component can be determined after optimization according to their first-order properties and third-order aberration targets. After a third optimization for minimum practical third-order aberrations of a zoom lens system, the aberration design using the thick lens module is complete, which provides a practical zoom lens system with thick lens structures. A double-sided telecentric zoom lens system is designed using the thick lens module in this paper, which shows that this method is practical for zoom lens design.

Nanoceria have no genotoxic effect on human lens epithelial cells

Energy Technology Data Exchange (ETDEWEB)

Pierscionek, Barbara K; Yasseen, Akeel A [School of Biomedical Sciences, University of Ulster, Coleraine, BT52 1SA (United Kingdom); Li, Yuebin; Schachar, Ronald A; Chen, Wei [Department of Physics, University of Texas at Arlington, Arlington, TX 76019 (United States); Colhoun, Liza M, E-mail: b.pierscionek@ulster.ac.uk, E-mail: weichen@uta.edu [Centre for Vision and Vascular Sciences, School of Medicine, Dentistry and Biomedical Sciences, Queen' s University Belfast, Grosvenor Road, Belfast, BT12 6BA (United Kingdom)

2010-01-22

There are no treatments for reversing or halting cataract, a disease of the structural proteins in the eye lens, that has associations with other age-related degenerative conditions such as Alzheimer's disease. The incidence of cataract and associated conditions is increasing as the average age of the population rises. Protein folding diseases are difficult to assess in vivo as proteins and their age-related changes are assessed after extraction. Nanotechnology can be used to investigate protein changes in the intact lens as well as for a potential means of drug delivery. Nanoparticles, such as cerium oxide (CeO{sub 2}) which have antioxidant properties, may even be used as a means of treating cataract directly. Prior to use in treatments, nanoparticle genotoxicity must be tested to assess the extent of any DNA or chromosomal damage. Sister chromatid exchanges were measured and DNA damage investigated using the alkaline COMET assay on cultured human lens epithelial cells, exposed to 5 and 10 {mu}g ml{sup -1} of CeO{sub 2} nanoparticles (nanoceria). Nanoceria at these dosages did not cause any DNA damage or significant increases in the number of sister chromatid exchanges. The absence of genotoxic effects on lens cells suggests that nanoceria, in the doses and exposures tested in this study, are not deleterious to the eye lens and have the potential for use in studying structural alterations, in developing non-surgical cataract treatments and in investigating other protein folding diseases.

Dynamic light scattering study on phase separation of a protein-water mixture: Application on cold cataract development in the ocular lens

Science.gov (United States)

Petta, V.; Pharmakakis, N.; Papatheodorou, G. N.; Yannopoulos, S. N.

2008-06-01

We present a detailed dynamic light scattering study of the phase separation in the ocular lens emerging during cold cataract development. Cold cataract is a phase separation effect that proceeds via spinodal decomposition of the lens cytoplasm with cooling. The intensity autocorrelation functions of the lens protein content are analyzed with the aid of two methods, providing information on the populations and dynamics of the scattering elements associated with cold cataract. It is found that the temperature dependence of many measurable parameters changes appreciably at the characteristic temperature ˜16±1°C which is associated with the onset of cold cataract. By extending the temperature range of this work to previously inaccessible regimes, i.e., well below the phase separation or coexistence curve at Tcc , we have been able to accurately determine the temperature dependence of the collective and self-diffusion coefficients of proteins near the spinodal. The analysis showed that the dynamics of proteins bears some resemblance to the dynamics of structural glasses, where the apparent activation energy for particle diffusion increases below Tcc , indicating a highly cooperative motion. Application of ideas developed for studying the critical dynamics of binary protein-solvent mixtures, as well as the use of a modified Arrhenius equation, enabled us to estimate the spinodal temperature Tsp of the lens nucleus. The applicability of dynamic light scattering as a noninvasive, early-diagnostic tool for ocular diseases is also demonstrated in light of the findings of the present paper.

Glycation precedes lens crystallin aggregation

International Nuclear Information System (INIS)

Swamy, M.S.; Perry, R.E.; Abraham, E.C.

1987-01-01

Non-enzymatic glycosylation (glycation) seems to have the potential to alter the structure of crystallins and make them susceptible to thiol oxidation leading to disulfide-linked high molecular weight (HMW) aggregate formation. They used streptozotocin diabetic rats during precataract and cataract stages and long-term cell-free glycation of bovine lens crystallins to study the relationship between glycation and lens crystallin aggregation. HMW aggregates and other protein components of the water-soluble (WS) and urea-soluble (US) fractions were separated by molecular sieve high performance liquid chromatography. Glycation was estimated by both [ 3 H]NaBH 4 reduction and phenylboronate agarose affinity chromatography. Levels of total glycated protein (GP) in the US fractions were about 2-fold higher than in the WS fractions and there was a linear increase in GP in both WS and US fractions. This increase was parallelled by a corresponding increase in HMW aggregates. Total GP extracted by the affinity method from the US fraction showed a predominance of HMW aggregates and vice versa. Cell-free glycation studies with bovine crystallins confirmed the results of the animals studies. Increasing glycation caused a corresponding increase in protein insolubilization and the insoluble fraction thus formed also contained more glycated protein. It appears that lens protein glycation, HMW aggregate formation, and protein insolubilization are interrelated

Myotonic dystrophy protein kinase (DMPK) induces actin cytoskeletal reorganization and apoptotic-like blebbing in lens cells

Science.gov (United States)

Jin, S.; Shimizu, M.; Balasubramanyam, A.; Epstein, H. F.

2000-01-01

DMPK, the product of the DM locus, is a member of the same family of serine-threonine protein kinases as the Rho-associated enzymes. In DM, membrane inclusions accumulate in lens fiber cells producing cataracts. Overexpression of DMPK in cultured lens epithelial cells led to apoptotic-like blebbing of the plasma membrane and reorganization of the actin cytoskeleton. Enzymatically active DMPK was necessary for both effects; inactive mutant DMPK protein did not produce either effect. Active RhoA but not constitutive GDP-state mutant protein produced similar effects as DMPK. The similar actions of DMPK and RhoA suggest that they may function in the same regulatory network. The observed effects of DMPK may be relevant to the removal of membrane organelles during normal lens differentiation and the retention of intracellular membranes in DM lenses. Copyright 2000 Wiley-Liss, Inc.

Active liquid-crystal deflector and lens with Fresnel structure

Science.gov (United States)

Shibuya, Giichi; Yamano, Shohei; Yoshida, Hiroyuki; Ozaki, Masanori

2017-02-01

A new type of tunable Fresnel deflector and lens composed of liquid crystal was developed. Combined structure of multiple interdigitated electrodes and the high-resistivity (HR) layer implements the saw-tooth distribution of electrical potential with only the planar surfaces of the transparent substrates. According to the numerical calculation and design, experimental devices were manufactured with the liquid crystal (LC) material sealed into the sandwiched flat glass plates of 0.7 mm thickness with rubbed alignment layers set to an anti-parallel configuration. Fabricated beam deflector with no moving parts shows the maximum tilt angle of +/-1.3 deg which can apply for optical image stabilizer (OIS) of micro camera. We also discussed and verified their lens characteristics to be extended more advanced applications. Transparent interdigitated electrodes were concentrically aligned on the lens aperture with the insulator gaps under their boundary area. The diameter of the lens aperture was 30 mm and the total number of Fresnel zone was 100. Phase retardation of the beam wavefront irradiated from the LC lens device can be evaluated by polarizing microscope images with a monochromatic filter. Radial positions of each observed fringe are plotted and fitted with 2nd degree polynomial approximation. The number of appeared fringes is over 600 in whole lens aperture area and the correlation coefficients of all approximations are over 0.993 that seems enough ideal optical wavefront. The obtained maximum lens powers from the approximations are about +/-4 m-1 which was satisfied both convex and concave lens characteristics; and their practical use for the tunable lens grade eyeglasses became more prospective.

Soluble lens protein polymorphism in flying fishes from the central Arabian Sea

Digital Repository Service at National Institute of Oceanography (India)

Menezes, M.R.

Soluble eye lens nuclei proteins of flying-fishes were studied by cellogel electrophoresis. Three distinct patterns characterized by the number of bands, mobility and staining intensity were observed. Morphological studies of these fishes showed...

Effect of infrared radiation on the lens

Directory of Open Access Journals (Sweden)

Aly Eman

2011-01-01

Full Text Available Background: Infrared (IR radiation is becoming more popular in industrial manufacturing processes and in many instruments used for diagnostic and therapeutic application to the human eye. Aim : The present study was designed to investigate the effect of IR radiation on rabbit′s crystalline lens and lens membrane. Materials and Methods: Fifteen New Zealand rabbits were used in the present work. The rabbits were classified into three groups; one of them served as control. The other two groups were exposed to IR radiation for 5 or 10 minutes. Animals from these two irradiated groups were subdivided into two subgroups; one of them was decapitated directly after IR exposure, while the other subgroup was decapitated 1 hour post exposure. IR was delivered from a General Electric Lamp model 250R 50/10, placed 20 cm from the rabbit and aimed at each eye. The activity of Na + -K + ATPase was measured in the lens membrane. Soluble lens proteins were extracted and the following measurements were carried out: estimation of total soluble protein, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE and Fourier transform infrared (FTIR spectroscopy. For comparison between multiple groups, analysis of variance was used with significance level set at P < 0.001. Results: The results indicated a change in the molecular weight of different lens crystalline accompanied with changes in protein backbone structure. These changes increased for the groups exposed to IR for 10 minutes. Moreover, the activity of Na + -K + ATPase significantly decreased for all groups. Conclusions: The protein of eye lens is very sensitive to IR radiation which is hazardous and may lead to cataract.

UVA Light-excited Kynurenines Oxidize Ascorbate and Modify Lens Proteins through the Formation of Advanced Glycation End Products

Science.gov (United States)

Linetsky, Mikhail; Raghavan, Cibin T.; Johar, Kaid; Fan, Xingjun; Monnier, Vincent M.; Vasavada, Abhay R.; Nagaraj, Ram H.

2014-01-01

Advanced glycation end products (AGEs) contribute to lens protein pigmentation and cross-linking during aging and cataract formation. In vitro experiments have shown that ascorbate (ASC) oxidation products can form AGEs in proteins. However, the mechanisms of ASC oxidation and AGE formation in the human lens are poorly understood. Kynurenines are tryptophan oxidation products produced from the indoleamine 2,3-dioxygenase (IDO)-mediated kynurenine pathway and are present in the human lens. This study investigated the ability of UVA light-excited kynurenines to photooxidize ASC and to form AGEs in lens proteins. UVA light-excited kynurenines in both free and protein-bound forms rapidly oxidized ASC, and such oxidation occurred even in the absence of oxygen. High levels of GSH inhibited but did not completely block ASC oxidation. Upon UVA irradiation, pigmented proteins from human cataractous lenses also oxidized ASC. When exposed to UVA light (320–400 nm, 100 milliwatts/cm2, 45 min to 2 h), young human lenses (20–36 years), which contain high levels of free kynurenines, lost a significant portion of their ASC content and accumulated AGEs. A similar formation of AGEs was observed in UVA-irradiated lenses from human IDO/human sodium-dependent vitamin C transporter-2 mice, which contain high levels of kynurenines and ASC. Our data suggest that kynurenine-mediated ASC oxidation followed by AGE formation may be an important mechanism for lens aging and the development of senile cataracts in humans. PMID:24798334

Photoaggregation of crystallins (main proteins of eye lens) under the effect of XeCl laser radiation

Science.gov (United States)

Soustov, Lev V.; Chelnokov, Evgeny V.; Bityurin, Nikita M.; Kiselev, A. L.; Nemov, V. V.; Sergeev, Yu. V.; Ostrovsky, Michail A.

2004-07-01

UV light is one of primary factors associated with cataract formation in the eye lens. α-, β-, γ-Crystallins maintain lens transparency, and damage to these proteins plays a major role in cataract formation. The effect of XeCl laser radiation (308 nm) on βL-crystallin solution is studied. The strong dependence of protein aggregation kinetics on both laser fluence (w) and repetition rate (F) is investigated. The kinetics features are similar to those of carbonic anhydrase photoaggregation studied previously.

Lipid-protein interactions in plasma membranes of fiber cells isolated from the human eye lens.

Science.gov (United States)

Raguz, Marija; Mainali, Laxman; O'Brien, William J; Subczynski, Witold K

2014-03-01

The protein content in human lens membranes is extremely high, increases with age, and is higher in the nucleus as compared with the cortex, which should strongly affect the organization and properties of the lipid bilayer portion of intact membranes. To assess these effects, the intact cortical and nuclear fiber cell plasma membranes isolated from human lenses from 41- to 60-year-old donors were studied using electron paramagnetic resonance spin-labeling methods. Results were compared with those obtained for lens lipid membranes prepared from total lipid extracts from human eyes of the same age group [Mainali, L., Raguz, M., O'Brien, W. J., and Subczynski, W. K. (2013) Biochim. Biophys. Acta]. Differences were considered to be mainly due to the effect of membrane proteins. The lipid-bilayer portions of intact membranes were significantly less fluid than lipid bilayers of lens lipid membranes, prepared without proteins. The intact membranes were found to contain three distinct lipid environments termed the bulk lipid domain, boundary lipid domain, and trapped lipid domain. However, the cholesterol bilayer domain, which was detected in cortical and nuclear lens lipid membranes, was not detected in intact membranes. The relative amounts of bulk and trapped lipids were evaluated. The amount of lipids in domains uniquely formed due to the presence of membrane proteins was greater in nuclear membranes than in cortical membranes. Thus, it is evident that the rigidity of nuclear membranes is greater than that of cortical membranes. Also the permeability coefficients for oxygen measured in domains of nuclear membranes were significantly lower than appropriate coefficients measured in cortical membranes. Relationships between the organization of lipids into lipid domains in fiber cells plasma membranes and the organization of membrane proteins are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gamma and x radiation and thermal neutrons effects in lens solutions and the relation with proteins concentration

International Nuclear Information System (INIS)

Ramirez A, M.; Alarcon C, A.

1996-01-01

Radiation effects have been studied irradiating porcine lens solutions with doses which range between 52 Gy to 1042 Gy in the case of x-rays (30 kVp), 631 Gy to 4001 Gy in the case of 60 Co gamma rays and 314 Gy to 7596 Gy for thermal neutrons. The optics density time variation of solutions was determined using a Spectronic-501 spectrophotometer, and with this data an equation which describes the behavior in the mentioned cases was found. A phenomenological model is postulated which connects the optical time variation density increment macroscopic effect with proteins concentration in the crystalline lens obtaining relative biological effectiveness using the supra-molecular aggregate formation due to the denaturalization and destruction of lens proteins by radiation criteria. (authors). 5 refs., 3 figs

Protective Effects of Acetylation on the Pathological Reactions of the Lens Crystallins with Homocysteine Thiolactone.

Directory of Open Access Journals (Sweden)

Zeinab Moafian

Full Text Available Various post-translational lens crystallins modifications result in structural and functional insults, contributing to the development of lens opacity and cataract disorders. Lens crystallins are potential targets of homocysteinylation, particularly under hyperhomocysteinemia which has been indicated in various eye diseases. Since both homocysteinylation and acetylation primarily occur on protein free amino groups, we applied different spectroscopic methods and gel mobility shift analysis to examine the possible preventive role of acetylation against homocysteinylation. Lens crystallins were extensively acetylated in the presence of acetic anhydride and then subjected to homocysteinylation in the presence of homocysteine thiolactone (HCTL. Extensive acetylation of the lens crystallins results in partial structural alteration and enhancement of their stability, as well as improvement of α-crystallin chaperone-like activity. In addition, acetylation partially prevents HCTL-induced structural alteration and aggregation of lens crystallins. Also, acetylation protects against HCTL-induced loss of α-crystallin chaperone activity. Additionally, subsequent acetylation and homocysteinylation cause significant proteolytic degradation of crystallins. Therefore, further experimentation is required in order to judge effectively the preventative role of acetylation on the structural and functional insults induced by homocysteinylation of lens crystallins.

Inter-specific and intraspecific eye lens protein differences in some sciaenid fishes from Goa coast

Digital Repository Service at National Institute of Oceanography (India)

Menezes, M.R.

Soluble eye lens nuclei proteins of sciaenid fishes were studied by cellogel electrophoresis. Four distinct patterns characterized by the number of bands, mobility and staining intensity were observed. Morphological studies of these fishes showed...

An electrophoretic study of the soluble lens proteins from the Indian mackerel, Rastrelliger kanagurta (Cuv)

Digital Repository Service at National Institute of Oceanography (India)

Menezes, M.R.

Soluble eye lens nuclei proteins of the Indian mackerel Rastrelliger kanagurta were studied by cellogel electrophoresis, to see whether there are any intra species variations. A distinct pattern characterised by the number of bands, mobility...

Submicron hollow spot generation by solid immersion lens and structured illumination

NARCIS (Netherlands)

Kim, M.S.; Assafrao, A.C.; Scharf, T.; Wachters, A.J.H.; Pereira, S.F.; Urbach, H.P.; Brun, M.; Olivier, S.; Nicoletti, S.; Herzig, H.P.

2012-01-01

We report on the experimental and numerical demonstration of immersed submicron-size hollow focused spots, generated by structuring the polarization state of an incident light beam impinging on a micro-size solid immersion lens (?-SIL) made of SiO2. Such structured focal spots are characterized by a

The Major Chromophore Arising from Glucose Degradation and Oxidative Stress Occurrence during Lens Proteins Glycation Induced by Glucose

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Felipe Ávila

2017-12-01

Full Text Available Glucose autoxidation has been proposed as a key reaction associated with deleterious effects induced by hyperglycemia in the eye lens. Little is known about chromophores generated during glucose autoxidation. In this study, we analyzed the effect of oxidative and dicarbonyl stress in the generation of a major chromophore arising from glucose degradation (GDC and its association with oxidative damage in lens proteins. Glucose (5 mM was incubated with H2O2 (0.5–5 mM, Cu2+ (5–50 μM, glyoxal (0.5–5 mM or methylglyoxal (0.5–5 mM at pH 7.4, 5% O2, 37 °C, from 0 to 30 days. GDC concentration increased with incubation time, as well as when incubated in the presence of H2O2 and/or Cu2+, which were effective even at the lowest concentrations. Dicarbonylic compounds did not increase the levels of GDC during incubations. 1H, 13C and FT-IR spectra from the purified fraction containing the chromophore (detected by UV/vis spectroscopy showed oxidation products of glucose, including gluconic acid. Lens proteins solutions (10 mg/mL incubated with glucose (30 mM presented increased levels of carboxymethyl-lysine and hydrogen peroxide that were associated with GDC increase. Our results suggest a possible use of GDC as a marker of autoxidative reactions occurring during lens proteins glycation induced by glucose.

Effects of x-irradiation on lens reducing systems

International Nuclear Information System (INIS)

Giblin, F.J.; Chakrapani, B.; Reddy, V.N.

1978-01-01

Studies have been made of the effects of x ray on various lens reducing systems including the levels of NADPH and glutathione (GSH), the activity of the hexose monophosphate shunt (HMS), and the activities of certain enzymes including glutathion reductase, glutathione peroxidase, and glucose-6-phosphate dehydrogenase (G-6-PD). It was found that during several weeks following x irradiation but prior to cataract formation there was very little change in the number of reduced -SH groups per unit weight of lens protein but that, with the appearance of cataract, there was a sudden loss of protein -SH groups. In contrast, the concentration of GSH in the x-rayed lens decreased throughout the experimental period. Similarly, the concentration of NADPH in the x-rayed lens was found to decrease significantly relative to controls one week prior to cataract formation and the ratio of NADPH to NADP + in the lens shifted at this time period from a value greater than 1.0 in the control lens to less than 1.0 in the x-rayed lens. A corresponding decrease occurred in the activity of the HMS in x-rayed lenses as measured by culture in the presence of 1- 14 C-labelled glucose. G-6-PD was partially inactivated in the x-rayed lens. Of the eight enzymes studied, G-6-PD appeared to be the most sensitive to x-irradiation. The data indicate that x-irradiation results in a steady decrease in the effectiveness of lens reducing systems and that, when these systems reach a critically low point, sudden oxidation of protein -SH groups and formation of high molecular weight protein aggregates may be initiated

Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

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Bradley Michael E

2006-02-01

Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

Chemical performance of multi-environment trials in lens (Lens culinaris M.).

Science.gov (United States)

Karadavut, Ufuk; Palta, Cetin

2010-01-15

Genotype-environment (GE) interaction has been a major effect to determine stable lens (Lens culinaris (Medik.) Merr.) cultivars for chemical composition in Turkey. Utilization of the lines depends on their agronomic traits and stability of the chemical composition in diverse environments. The objectives of this study were: (i) to evaluate the influence of year and location on the chemical composition of lens genotypes; and (ii) to determine which cultivar is the most stable. Genotypes were evaluated over 3 years (2005, 2006 and 2007) at four locations in Turkey. Effects of year had the largest impact on all protein contents. GE interaction was analyzed by using linear regression techniques. Stability was estimated using the Eberhart and Russell method. 'Kişlik Kirmizi51' was the most stable cultivar for grain yield. The highest protein was obtained from 'Kişlik Kirmizi51' (4.6%) across environments. According to stability analysis, 'Firat 87' had the most stable chemical composition. This genotype had a regression coefficient (b(i) = 1) around unity, and deviations from regression values (delta(ij) = 0) around zero. Chemical composition was affected by year in this study. Temperature might have an effect on protein, oil, carbohydrate, fibre and ash. Firat 87 could be recommended for favourable environments. Copyright (c) 2009 Society of Chemical Industry.

Comparison of lens oxidative damage induced by vitrectomy and/or hyperoxia in rabbits

Directory of Open Access Journals (Sweden)

Hong Yan

2017-02-01

Full Text Available AIM: To compare of lens oxidative damage induced by vitrectomy and/or hyperoxia in rabbit. METHODS: Sixteen New Zealand rabbits (2.4-2.5 kg were randomly divided into two groups (Group A, n=12; Group B, n=4. In Group A, the right eyes were treated with vitrectomy and systemic hyperoxia (oxygen concentration: 80%-85%, 1 ATA, 4h/d (Group A-right, and the left eyes were treated with hyperoxia without vitrectomy surgery (Group A-left. Four rabbits in group B (eight eyes were untreated as the controls. Lens transparency was monitored with a slit lamp and recorded before and after vitrectomy. After hyperoxic treatment for 6mo, the eyeballs were removed and the lens cortices (containing the capsules and nuclei were separated for further morphological and biochemical evaluation. RESULTS: Six months after treatments, there were no significant morphological changes in the lenses in any experimental group when observed with a slit lamp. However, the levels of water-soluble proteins and ascorbate, and the activities of catalase and Na+-K+-ATPase were significantly reduced, whereas the levels of malondialdehyde and transforming growth factor β2 (TGF-β2 were significantly elevated, in both the cortices and nuclei of eyes treated with vitrectomy and hyperoxia. The increase in protein-glutathione mixed disulfides and the reduction in water-soluble proteins were more obvious in the lens nuclei. The levels of ascorbate in the vitreous fluid were also reduced after vitrectomy, whereas TGF-β2 increased after vitrectomy and hyperoxia. Systemic hyperoxia exposure increased these effects. CONCLUSION: Removal of the intact vitreous gel with vitrectomy and exposing the lens to increased oxygen from the retina induce lens oxidation and aggregation. Thus, an intact vitreous gel structure may protect the lens from oxidative insult and maintain lens transparency.

Effects of x-irradiation on lens reducing systems. [Rabbits

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Giblin, F.J.; Chakrapani, B.; Reddy, V.N.

1978-01-01

Studies have been made of the effects of x ray on various lens reducing systems including the levels of NADPH and glutathione (GSH), the activity of the hexose monophosphate shunt (HMS), and the activities of certain enzymes including glutathion reductase, glutathione peroxidase, and glucose-6-phosphate dehydrogenase (G-6-PD). It was found that during several weeks following x irradiation but prior to cataract formation there was very little change in the number of reduced -SH groups per unit weight of lens protein but that, with the appearance of cataract, there was a sudden loss of protein -SH groups. In contrast, the concentration of GSH in the x-rayed lens decreased throughout the experimental period. Similarly, the concentration of NADPH in the x-rayed lens was found to decrease significantly relative to controls one week prior to cataract formation and the ratio of NADPH to NADP/sup +/ in the lens shifted at this time period from a value greater than 1.0 in the control lens to less than 1.0 in the x-rayed lens. A corresponding decrease occurred in the activity of the HMS in x-rayed lenses as measured by culture in the presence of 1-/sup 14/C-labelled glucose. G-6-PD was partially inactivated in the x-rayed lens. Of the eight enzymes studied, G-6-PD appeared to be the most sensitive to x-irradiation. The data indicate that x-irradiation results in a steady decrease in the effectiveness of lens reducing systems and that, when these systems reach a critically low point, sudden oxidation of protein -SH groups and formation of high molecular weight protein aggregates may be initiated.

Photosensitized oxidation in the ocular lens: evidence for photosensitizers endogenous to the human lens

International Nuclear Information System (INIS)

Zigler, J.S. Jr.; Goosey, J.D.

1981-01-01

Numerous investigators have attempted to associate near UV light exposure with various changes which occur to lens crystallins during aging and cataractogenesis. Recently it was shown that in vitro singlet oxygen mediated oxidation of lens crystallins produces effects very similar to those documented for crystallins from old or cataractous lenses and it was suggested that near UV photodynamic effects may play a major role in vivo in aging in the human lens. It has now been shown that certain oxidation products of tryptophan which have been identified in human lens can act as near UV photosensitizers, producing singlet oxygen. The insoluble protein fraction from human cataracts was shown to have the capacity to act as a photosensitizer. An age-related increase in photosensitizing capacity was also demonstrated in the soluble crystallins from human lens. These findings are discussed with respect to development of pigmented nuclear cataracts. (author)

Surface modification of fluorosilicone acrylate RGP contact lens via low-temperature argon plasma

International Nuclear Information System (INIS)

Yin Shiheng; Wang Yingjun; Ren Li; Zhao Lianna; Kuang Tongchun; Chen Hao; Qu Jia

2008-01-01

A fluorosilicone acrylate rigid gas permeable (RGP) contact lens was modified via argon plasma to improve surface hydrophilicity and resistance to protein deposition. The influence of plasma treatment on surface chemical structure, hydrophilicity and morphology of RGP lens was investigated by X-ray photoelectron spectrometer (XPS), contact angle measurements and scanning electron microscope (SEM), respectively. The contact angle results showed that the hydrophilicity of the contact lens was improved after plasma treatment. XPS results indicated that the incorporation of oxygen-containing groups on surface and the transformation of silicone into hydrophilic silicate after plasma treatment are the main reasons for the surface hydrophilicity improvement. SEM results showed that argon plasma with higher power could lead to surface etching

The effects of actomyosin disruptors on the mechanical integrity of the avian crystalline lens.

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Won, Gah-Jone; Fudge, Douglas S; Choh, Vivian

2015-01-01

Actin and myosin within the crystalline lens maintain the structural integrity of lens fiber cells and form a hexagonal lattice cradling the posterior surface of the lens. The actomyosin network was pharmacologically disrupted to examine the effects on lenticular biomechanics and optical quality. One lens of 7-day-old White Leghorn chickens was treated with 10 µM of a disruptor and the other with 0.01% dimethyl sulfoxide (vehicle). Actin, myosin, and myosin light chain kinase (MLCK) disruptors were used. The stiffness and the optical quality of the control and treated lenses were measured. Western blotting and confocal imaging were used to confirm that treatment led to a disruption of the actomyosin network. The times for the lenses to recover stiffness to match the control values were also measured. Disruptor-treated lenses were significantly less stiff than their controls (p≤0.0274 for all disruptors). The disruptors led to changes in the relative protein amounts as well as the distributions of proteins within the lattice. However, the disruptors did not affect the clarity of the lenses (p≥0.4696 for all disruptors), nor did they affect spherical aberration (p = 0.02245). The effects of all three disruptors were reversible, with lenses recovering from treatment with actin, myosin, and MLCK disruptors after 4 h, 1 h, and 8 min, respectively. Cytoskeletal protein disruptors led to a decreased stiffness of the lens, and the effects were reversible. Optical quality was mostly unaffected, but the long-term consequences remain unclear. Our results raise the possibility that the mechanical properties of the avian lens may be actively regulated in vivo via adjustments to the actomyosin lattice.

Analysis of the post-translational modifications of the individual amino acids in lens proteins which were induced by aging and irradiation

International Nuclear Information System (INIS)

Fujii, Noriko; Kim, Ingu; Saito, Takeshi; Takata, Takumi

2017-01-01

The eye lens is a transparent organ that functions to focus light and images on the retina. The transparency and high refraction of the lens are maintained by the function of α-, β- and γ-crystallins. These long-lived proteins are subject to various post-translational modifications, such as oxidation, deamidation, truncation and isomerization, which occur gradually during the aging process. Such modifications, which are generated by UV light and oxidative stress, decrease crystallin solubility and lens transparency, and ultimately lead to the development of age-related cataracts. Here, we irradiated young rat lenses with γ-rays (5-500 Gy) and extracted the water-soluble (WS) and insoluble (WI) protein fractions. The WS and WI lens proteins were digested with trypsin, and the resulting peptides were analyzed by one-shot LC-MS/MS to determine the specific sites of oxidation of methionine and tryptophan, deamidation of asparagine and glutamine, and isomerization of aspartyl in rat α- and β-crystallins in the WS and WI fractions. Oxidation and deamidation occurred in several crystallins after irradiation at more than, respectively, 50 Gy and 5 Gy; however, isomerization did not occur in any crystallin even after exposure to 500 Gy of irradiation. The number of oxidation and deamidation sites was much higher in the WI than in the WS fraction. Furthermore, the oxidation and deamidation sites in rat crystallins resemble those reported in crystallins from human age-related cataracts. Thus, this study on post-translational modifications of crystallins induced by ionizing irradiation may provide useful information relevant to the formation of human age-related cataracts. (author)

The status of intercellular junctions in established lens epithelial cell lines.

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Dave, Alpana; Craig, Jamie E; Sharma, Shiwani

2012-01-01

Cataract is the major cause of vision-related disability worldwide. Mutations in the crystallin genes are the most common known cause of inherited congenital cataract. Mutations in the genes associated with intercellular contacts, such as Nance-Horan Syndrome (NHS) and Ephrin type A receptor-2 (EPHA2), are other recognized causes of congenital cataract. The EPHA2 gene has been also associated with age-related cataract, suggesting that intercellular junctions are important in not only lens development, but also in maintaining lens transparency. The purpose of this study was to analyze the expression and localization of the key cell junction and cytoskeletal proteins, and of NHS and EPHA2, in established lens epithelial cell lines to determine their suitability as model epithelial systems for the functional investigation of genes involved in intercellular contacts and implicated in cataract. The expression and subcellular localization of occludin and zona occludens protein-1 (ZO-1), which are associated with tight junctions; E-cadherin, which is associated with adherence junctions; and the cytoskeletal actin were analyzed in monolayers of a human lens epithelial cell line (SRA 01/04) and a mouse lens epithelial cell line (αTN4). In addition, the expression and subcellular localization of the NHS and EPHA2 proteins were analyzed in these cell lines. Protein or mRNA expression was respectively determined by western blotting or reverse transcription-polymerase chain reaction (RT-PCR), and localization was determined by immunofluorescence labeling. Human SRA 01/04 and mouse αTN4 lens epithelial cells expressed either the proteins of interest or their encoding mRNA. Occludin, ZO-1, and NHS proteins localized to the cellular periphery, whereas E-cadherin, actin, and EPHA2 localized in the cytoplasm in these cell lines. The human SRA 01/04 and mouse αTN4 lens epithelial cells express the key junctional proteins. The localization patterns of these proteins suggest that

A novel lens epithelium gene, LEP503, is highly conserved in different vertebrate species and is developmentally regulated in postnatal rat lens.

Science.gov (United States)

Wen, Y; Sachs, G; Athmann, C

2000-02-01

The development of the lens is dependent on the proliferation of lens epithelial cells and their differentiation into fiber cells near the lens bow/equator. Identification of genes specifically expressed in the lens epithelial cells and their functions may provide insight into molecular events that regulate the processes of lens epithelial cell differentiation. In this study, a novel lens epithelium gene product, LEP503, identified from rat by a subtractive cDNA cloning strategy was investigated in the genome organization, mRNA expression and protein localization. The genomic sequences for LEP503 isolated from rat, mouse and human span 1754 bp, 1694 bp and 1895 bp regions encompassing the 5'-flanking region, two exons, one intron and 3'-flanking region. All exon-intron junction sequences conform to the GT/AG rule. Both mouse and human LEP503 genes show very high identity (93% for mouse and 79% for human) to rat LEP503 gene in the exon 1 that contains an open reading frame coding for a protein of 61 amino acid residues with a leucine-rich domain. The deduced protein sequences also show high identity (91% between mouse and rat and 77% between human and rat). Western blot shows that LEP503 is present as a specific approximately 6.9 kDa band in the water-insoluble-urea-soluble fraction of lens cortex where lens epithelium is included. Immuno-staining shows that LEP503 is localized in the epithelial cells along the entire anterior surface of rat lens. Developmentally, LEP503 is expressed at a low level at newborn, and then the expression level increases by about ten-fold around postnatal day 14 and remains at this high level for about 25 days before it drops back to the low level by postnatal day 84. These data suggest that the LEP503 may be an important lens epithelial cell gene involving the processes of epithelial cell differentiation. Copyright 2000 Academic Press.

The sloan lens acs survey. II. Stellar populations and internal structure of early-type lens galaxies

NARCIS (Netherlands)

Treu, Tommaso; Koopmans, Léon V.; Bolton, Adam S.; Burles, Scott; Moustakas, Leonidas A.

2006-01-01

We use HST images to derive effective radii and effective surface brightnesses of 15 early-type (E+S0) lens galaxies identified by the SLACS Survey. Our measurements are combined with stellar velocity dispersions from the SDSS database to investigate for the first time the distribution of lens

Gamma crystallins of the human eye lens.

Science.gov (United States)

Vendra, Venkata Pulla Rao; Khan, Ismail; Chandani, Sushil; Muniyandi, Anbukkarasi; Balasubramanian, Dorairajan

2016-01-01

Protein crystallins co me in three types (α, β and γ) and are found predominantly in the eye, and particularly in the lens, where they are packed into a compact, plastic, elastic, and transparent globule of proper refractive power range that aids in focusing incoming light on to the retina. Of these, the γ-crystallins are found largely in the nuclear region of the lens at very high concentrations (>400 mg/ml). The connection between their structure and inter-molecular interactions and lens transparency is an issue of particular interest. We review the origin and phylogeny of the gamma crystallins, their special structure involving the use of Greek key supersecondary structural motif, and how they aid in offering the appropriate refractive index gradient, intermolecular short range attractive interactions (aiding in packing them into a transparent ball), the role that several of the constituent amino acid residues play in this process, the thermodynamic and kinetic stability and how even single point mutations can upset this delicate balance and lead to intermolecular aggregation, forming light-scattering particles which compromise transparency. We cite several examples of this, and illustrate this by cloning, expressing, isolating and comparing the properties of the mutant protein S39C of human γS-crystallin (associated with congenital cataract-microcornea), with those of the wild type molecule. In addition, we note that human γ-crystallins are also present in other parts of the eye (e.g., retina), where their functions are yet to be understood. There are several 'crucial' residues in and around the Greek key motifs which are essential to maintain the compact architecture of the crystallin molecules. We find that a mutation that replaces even one of these residues can lead to reduction in solubility, formation of light-scattering particles and loss of transparency in the molecular assembly. Such a molecular understanding of the process helps us construct the

Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

International Nuclear Information System (INIS)

Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

2008-01-01

A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH 2 -terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH 2 -terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 78.6, c = 135.2 Å

Human lens colouration, age and cataract

International Nuclear Information System (INIS)

Truscott, R.J.W.; Garner, B.; Hood, B.

1999-01-01

Full text: The human lens biosynthesises UV filter compounds which effectively remove light in the 300-400nm band. These chemicals are present either as an aid to visual acuity, or to filter out damaging UV radiation. The primate UV filters are 3-hydroxykynurenine analogues derived from the metabolism of tryptophan. We have recently demonstrated that these endogenous UV filters are not innocuous, but are in fact capable of binding to proteins, including the crystalline proteins which make up the bulk of the lens. Thus, over time, the levels of protein - bound UV filters increase and this results in the human lens becoming progressively more yellow as we age. This colouration affects our colour vision and it may also be responsible for the brown colour of lenses which is the hallmark of age-related nuclear cataract. An understanding of the intrinsic instability of the endogenous UV filters, combined with changes in the internal transport of these and other small molecular weight compounds including antioxidants, such as glutathione, is allowing us to gain an insight into the processes responsible for the development of age-related cataract: the major cause of world blindness

Transglutaminase involvement in UV-A damage to the eye lens

International Nuclear Information System (INIS)

Weinreb, Orly; Dovrat, A.

1996-01-01

Solar radiation is believed to be one of the major environmental factors involved in lens cataractogenesis. The purpose of the study was to investigate the mechanisms by which UV-A at 365 nm causes damage to the eye lens. Bovine lenses were placed in special culture cells for pre-incubation of 24 hr. The lenses were positioned so that the anterior surface faced the incident UV-A radiation source and were maintained in the cells during irradiation. After irradiation, lens optical quality was monitored throughout the culture period and lens epithelium, cortex and nuclear samples were taken for biochemical analysis. Transglutaminase activity in the lens was affected by the radiation. The activity of transglutaminase in lens epithelium cortex and nucleus increased as a result of the irradiation and then declined towards control levels during the culture period, as the lens recovered from the UV-A damage. Specific lens proteins αB and βB1 crystallins (the enzyme substrates) were analyzed by SDS polyacrylamid gel electrophoreses and immunoblotting with specific antibodies. Seventy-two hours after irradiation of 44.8 J cm -2 UV-A, αB crystallins were affected as was shown by the appearance of aggregation and degradation products. Some protein changes seem to be reversible. It appears that transglutaminase may be involved in the mechanism by which UV-A causes damage to the eye lens. (Author)

The lens and cataracts.

Science.gov (United States)

Matthews, Andrew G

2004-08-01

It is conservatively estimated that some form of lens opacity is present in 5% to 7% of horses with otherwise clinically normal eyes.These opacities can range from small epicapsular remnants of the fetal vasculature to dense and extensive cataract. A cataract is defined technically as any opacity or alteration in the optical homogeneity of the lens involving one or more of the following: anterior epithelium, capsule, cortex, or nucleus. In the horse, cataracts rarely involve the entire lens structure (ie, complete cataracts) and are more usually localized to one anatomic landmark or sector of the lens. Complete cataracts are invariably associated with overt and significant visual disability. Focal or incomplete cataracts alone seldom cause any apparent visual dysfunction in affected horses,however.

Transverse-structure electrostatic charged particle beam lens

Science.gov (United States)

Moran, M.J.

1998-10-13

Electrostatic particle-beam lenses using a concentric co-planar array of independently biased rings can be advantageous for some applications. Traditional electrostatic lenses often consist of axial series of biased rings, apertures, or tubes. The science of lens design has devoted much attention to finding axial arrangements that compensate for the substantial optical aberrations of the individual elements. Thus, as with multi-element lenses for light, a multi-element charged-particle lens can have optical behavior that is far superior to that of the individual elements. Transverse multiple-concentric-ring lenses achieve high performance, while also having advantages in terms of compactness and optical versatility. 7 figs.

Protein Structure Prediction by Protein Threading

Science.gov (United States)

Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

Microscopic and spectroscopic investigation of an explanted opacified intraocular lens

Energy Technology Data Exchange (ETDEWEB)

Simon, V., E-mail: viosimon@phys.ubbcluj.ro [Babeş-Bolyai University, Faculty of Physics and Interdisciplinary Research Institute on Bio-Nano-Sciences, 400084 Cluj-Napoca (Romania); Radu, T.; Vulpoi, A. [Babeş-Bolyai University, Faculty of Physics and Interdisciplinary Research Institute on Bio-Nano-Sciences, 400084 Cluj-Napoca (Romania); Rosca, C. [Optilens Clinic of Ophthalmology, 400604 Cluj-Napoca (Romania); Eniu, D. [Iuliu Haţieganu University of Medicine and Pharmacy, Department of Molecular Sciences, 400349 Cluj-Napoca (Romania)

2015-01-15

Highlights: • Changes on intraocular lens (IOL) surface after implantation. • Partial opacification of IOL central area. • Elemental composition on IOL surface prior to and after implantation. • First XPS depth profiling examination of the opacifying deposits. • Cell-mediated hydroxyapatite structuring. - Abstract: The investigated polymethylmethacrylate intraocular lens explanted an year after implantation presented a fine granularity consisting of ring-like grains of about 15 μm in diameter. In order to evidence the changes occurred on intraocular lens relative to morphology, elemental composition and atomic environments, microscopic and spectroscopic analyses were carried out using scanning electron microscopy (SEM), Fourier transform infrared (FTIR), energy-dispersive X-ray (EDS), and X-ray photoelectron (XPS) spectroscopies. The results revealed that the grains contain hydroxyapatite mineral phase. A protein layer covers the lens both in opacified and transparent zones. The amide II band is like in basal epithelial cells. The shape and size of the grains, and the XPS depth profiling results indicate the possibility of a cell-mediated process involving lens epithelial cells which fagocitated apoptotic epithelial cells, and in which the debris derived from cell necrosis were calcified. To the best of our knowledge, this is the first investigation on explanted intraocular lenses using XPS depth profiling in order to examine the inside of the opacifying deposits.

The Role of Aquaporins in Ocular Lens Homeostasis

Science.gov (United States)

Schey, Kevin L.; Petrova, Rosica S.; Gletten, Romell B.; Donaldson, Paul J.

2017-01-01

Aquaporins (AQPs), by playing essential roles in the maintenance of ocular lens homeostasis, contribute to the establishment and maintenance of the overall optical properties of the lens over many decades of life. Three aquaporins, AQP0, AQP1 and AQP5, each with distinctly different functional properties, are abundantly and differentially expressed in the different regions of the ocular lens. Furthermore, the diversity of AQP functionality is increased in the absence of protein turnover by age-related modifications to lens AQPs that are proposed to alter AQP function in the different regions of the lens. These regional differences in AQP functionality are proposed to contribute to the generation and directionality of the lens internal microcirculation; a system of circulating ionic and fluid fluxes that delivers nutrients to and removes wastes from the lens faster than could be achieved by passive diffusion alone. In this review, we present how regional differences in lens AQP isoforms potentially contribute to this microcirculation system by highlighting current areas of investigation and emphasizing areas where future work is required. PMID:29231874

Single lens to lens duplication: The missing link

OpenAIRE

Bhatt, Rupal; Jethani, Jitendra; Saluja, Praveen; Bharti, Vinay

2008-01-01

Congenital anomalies of the lens include a wide range from lens coloboma to primary aphakia and doubling of lens. There have been few case reports of double lens; the etiology suggested is metaplastic changes in the surface ectoderm that leads to formation of two lens vesicles and hence resulting in double lens. We report a case with bilobed lens, which raises the possibility of explaining the etiology of double lens.

Effects of lens extirpation with anterior vitrectomy on vitreous three-dimensional mesh structure

Directory of Open Access Journals (Sweden)

Yan Zhao

2017-06-01

Full Text Available AIM: To investigate the changes in vitreous gel structure after lens extirpation combined with anterior vitrectomy in rabbit eyes. METHODS: Twenty-eight chinchilla rabbits were divided into three groups. The control group (Group I included 16 eyes from eight rabbits who did not receive any treatment. Group II included 20 eyes from 10 rabbits that underwent lens aspiration only. Group III included 20 eyes from 10 rabbits that underwent lens aspiration combined with posterior capsulotomy and anterior vitrectomy. Eyes were harvested on the 30th and 60th day postoperatively, respectively. Changes in vitreous gel stretch length due to gravity and the rate of vitreous liquefaction were observed. The collagen content in the vitreous body was examined using the L-hydroxyproline test. Electronic microscopic images were obtained from each eyeball. RESULTS: On both the 30th and 60th day postoperatively, the vitreous gel length of group III was significantly shorter than group I and group II (P<0.05, while the rate of liquefaction of the vitreous body in group III was significantly higher than group I and group II (P<0.05. The collagen content in group III was also higher than that in group I and group II (P<0.05. CONCLUSION: Loss of vitreous gel mass is more likely to occur in the eyes of rabbits receiving anterior vitrectomy. Lensectomy combined with anterior vitrectomy may damage the stable three-dimensional mesh structure of collagen, which could aggravate vitreous gel liquefaction.

Structural deformation upon protein-protein interaction: a structural alphabet approach.

Science.gov (United States)

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-02-28

In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

Structural deformation upon protein-protein interaction: A structural alphabet approach

Directory of Open Access Journals (Sweden)

Lecornet Hélène

2008-02-01

Full Text Available Abstract Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%. This proportion is even greater in the interface regions (41%. Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

Orbiting objective lens telescope system and method

International Nuclear Information System (INIS)

Crooks, J.W. Jr.

1984-01-01

A large objective lens is placed in a highly eccentric orbit about the earth. The orbit and orientation of the lens are carefully chosen so that it focuses light or other radiation from a preselected astronomical object into an image which slowly moves across the surface of the earth. A row of optical sensing units is located on the surface of the earth so that the image focused by the orbiting objective lens will travel substantially perpendicularly across the row during an observation. Output data generated from the sensing units may be multiplexed and fed to a real time processor which produces display signals. Each of the sensing units provides one scan line of the image being observed. The display signals are fed to a suitable display device which produces a picture of the preselected astronomical object. The objective lens may comprise a large flexible Fresnel zone plate or a flexible convex lens carried by a bicycle wheel-type supporting structure. The lens and supporting structure may be unfolded from compact cargo configurations and rotated after being placed into orbit

Proteomic Analysis of Lipid Raft-Like Detergent-Resistant Membranes of Lens Fiber Cells.

Science.gov (United States)

Wang, Zhen; Schey, Kevin L

2015-12-01

Plasma membranes of lens fiber cells have high levels of long-chain saturated fatty acids, cholesterol, and sphingolipids-key components of lipid rafts. Thus, lipid rafts are expected to constitute a significant portion of fiber cell membranes and play important roles in lens biology. The purpose of this study was to characterize the lens lipid raft proteome. Quantitative proteomics, both label-free and iTRAQ methods, were used to characterize lens fiber cell lipid raft proteins. Detergent-resistant, lipid raft membrane (DRM) fractions were isolated by sucrose gradient centrifugation. To confirm protein localization to lipid rafts, protein sensitivity to cholesterol removal by methyl-β-cyclodextrin was quantified by iTRAQ analysis. A total of 506 proteins were identified in raft-like detergent-resistant membranes. Proteins identified support important functions of raft domains in fiber cells, including trafficking, signal transduction, and cytoskeletal organization. In cholesterol-sensitivity studies, 200 proteins were quantified and 71 proteins were strongly affected by cholesterol removal. Lipid raft markers flotillin-1 and flotillin-2 and a significant fraction of AQP0, MP20, and AQP5 were found in the DRM fraction and were highly sensitive to cholesterol removal. Connexins 46 and 50 were more abundant in nonraft fractions, but a small fraction of each was found in the DRM fraction and was strongly affected by cholesterol removal. Quantification of modified AQP0 confirmed that fatty acylation targeted this protein to membrane raft domains. These data represent the first comprehensive profile of the lipid raft proteome of lens fiber cells and provide information on membrane protein organization in these cells.

Photoreactivity of biologically active compounds. VIII. Photosensitized polymerization of lens proteins by antimalarial drugs in vitro.

Science.gov (United States)

Kristensen, S; Wang, R H; Tønnesen, H H; Dillon, J; Roberts, J E

1995-02-01

The drugs commonly used in the treatment of malaria are photochemically unstable. Several of these compounds cause dermal and ocular toxic reactions that may be light induced. The in vitro photopolymerization of calf lens proteins in the presence of antimalarial drugs was studied as part of a screening of the photochemical properties and phototoxic capabilities of these compounds. The pseudo-first-order rate constant for the reaction was calculated, and related to the amount of light absorbed by the compounds in order to determine the relative photosensitizing effect of each drug. The reaction mechanisms were evaluated by adding a variety of quenchers to the reaction medium during irradiation. Based on the results obtained in this study and previous knowledge about the pharmacokinetic behavior of these compounds, several of the drugs investigated have to be considered as potential photosensitizers in the human lens, the retina and the skin.

Lens proteome map and alpha-crystallin profile of the catfish Rita rita.

Science.gov (United States)

Mohanty, Bimal Prasanna; Bhattacharjee, Soma; Das, Manas Kumar

2011-02-01

Crystallins are a diverse group of proteins that constitute nearly 90% of the total soluble proteins of the vertebrate eye lens and these tightly packed crystallins are responsible for transparency of the lens. These proteins have been studied in different model and non-model species for understanding the modifications they undergo with ageing that lead to cataract, a disease of protein aggregation. In the present investigation, we studied the lens crystallin profile of the tropical freshwater catfish Rita rita. Profiles of lens crystallins were analyzed and crystallin proteome maps of Rita rita were generated for the first time. alphaA-crystallins, member of the alpha-crystallin family, which are molecular chaperons and play crucial role in maintaining lens transparency were identified by 1- and 2-D immunoblot analysis with anti-alphaA-crystallin antibody. Two protein bands of 19-20 kDa were identified as alphaA-crystallins on 1-D immunoblots and these bands separated into 10 discrete spots on 2-D immunoblot. However, anti-alphaB-crystallin and antiphospho-alphaB-crystallin antibodies were not able to detect any immunoreactive bands on 1- and 2-D immunoblots, indicating alphaB-crystallin was either absent or present in extremely low concentration in Rita rita lens. Thus, Rita rita alpha-crystallins are more like that of the catfish Clarias batrachus and the mammal kangaroo in its alphaA- and alphaB-crystallin content (contain low amount from 5-9% of alphaB-crystallin) and unlike the dogfish, zebrafish, human, bovine and mouse alpha-crystallins (contain higher amount of alphaB-crystallin from 25% in mouse and bovine to 85% in dogfish). Results of the present study can be the baseline information for stimulating further investigation on Rita rita lens crystallins for comparative lens proteomics. Comparing and contrasting the alpha-crystallins of the dogfish and Rita rita may provide valuable information on the functional attributes of alphaA- and alphaB-isoforms, as

Algorithm design of liquid lens inspection system

Science.gov (United States)

Hsieh, Lu-Lin; Wang, Chun-Chieh

2008-08-01

In mobile lens domain, the glass lens is often to be applied in high-resolution requirement situation; but the glass zoom lens needs to be collocated with movable machinery and voice-coil motor, which usually arises some space limits in minimum design. In high level molding component technology development, the appearance of liquid lens has become the focus of mobile phone and digital camera companies. The liquid lens sets with solid optical lens and driving circuit has replaced the original components. As a result, the volume requirement is decreased to merely 50% of the original design. Besides, with the high focus adjusting speed, low energy requirement, high durability, and low-cost manufacturing process, the liquid lens shows advantages in the competitive market. In the past, authors only need to inspect the scrape defect made by external force for the glass lens. As to the liquid lens, authors need to inspect the state of four different structural layers due to the different design and structure. In this paper, authors apply machine vision and digital image processing technology to administer inspections in the particular layer according to the needs of users. According to our experiment results, the algorithm proposed can automatically delete non-focus background, extract the region of interest, find out and analyze the defects efficiently in the particular layer. In the future, authors will combine the algorithm of the system with automatic-focus technology to implement the inside inspection based on the product inspective demands.

Vitamin C degradation products and pathways in the human lens.

Science.gov (United States)

Nemet, Ina; Monnier, Vincent M

2011-10-28

Vitamin C and its degradation products participate in chemical modifications of proteins in vivo through non-enzymatic glycation (Maillard reaction) and formation of different products called advanced glycation end products. Vitamin C levels are particularly high in selected tissues, such as lens, brain and adrenal gland, and its degradation products can inflict substantial protein damage via formation of advanced glycation end products. However, the pathways of in vivo vitamin C degradation are poorly understood. Here we have determined the levels of vitamin C oxidation and degradation products dehydroascorbic acid, 2,3-diketogulonic acid, 3-deoxythreosone, xylosone, and threosone in the human lens using o-phenylenediamine to trap both free and protein-bound adducts. In the protein-free fraction and water-soluble proteins (WSP), all five listed degradation products were identified. Dehydroascorbic acid, 2,3-diketogulonic acid, and 3-deoxythreosone were the major products in the protein-free fraction, whereas in the WSP, 3-deoxythreosone was the most abundant measured dicarbonyl. In addition, 3-deoxythreosone in WSP showed positive linear correlation with age (p degradation product bound to human lens proteins provides in vivo evidence for the non-oxidative pathway of dehydroascorbate degradation into erythrulose as a major pathway for vitamin C degradation in vivo.

Photonic crystal based polarization insensitive flat lens

International Nuclear Information System (INIS)

Turduev, M; Bor, E; Kurt, H

2017-01-01

The paper proposes a new design of an inhomogeneous artificially created photonic crystal lens structure consisting of annular dielectric rods to efficiently focus both transverse electric and transverse magnetic polarizations of light into the same focal point. The locations of each individual cell that contains the annular dielectric rods are determined according to a nonlinear distribution function. The inner and outer radii of the annular photonic dielectric rods are optimized with respect to the polarization insensitive frequency response of the transmission spectrum of the lens structure. The physical background of the polarization insensitive focusing mechanism is investigated in both spatial and frequency domains. Moreover, polarization independent wavefront transformation/focusing has been explored in detail by investigating the dispersion relation of the structure. Corresponding phase index distribution of the lens is attained for polarization insensitive normalized frequency range of a / λ   =  0.280 and a / λ   =  0.300, where a denotes the lattice constant of the designed structure and λ denotes the wavelength of the incident light. We show the wave transformation performance and focal point movement dynamics for both polarizations of the lens structure by specially adjusting the length of the structure. The 3D finite-difference time domain numerical analysis is also performed to verifiy that the proposed design is able to focus the wave regardless of polarization into approximately the same focal point (difference between focal distances of both polarizations stays below 0.25 λ ) with an operating bandwidth of 4.30% between 1476 nm and 1541 nm at telecom wavelengths. The main superiorities of the proposed lens structure are being all dielectric and compact, and having flat front and back surfaces, rendering the proposed lens design more practical in the photonic integration process in various applications such as optical switch

Particle swarm optimization applied to automatic lens design

Science.gov (United States)

Qin, Hua

2011-06-01

This paper describes a novel application of Particle Swarm Optimization (PSO) technique to lens design. A mathematical model is constructed, and merit functions in an optical system are employed as fitness functions, which combined radiuses of curvature, thicknesses among lens surfaces and refractive indices regarding an optical system. By using this function, the aberration correction is carried out. A design example using PSO is given. Results show that PSO as optical design tools is practical and powerful, and this method is no longer dependent on the lens initial structure and can arbitrarily create search ranges of structural parameters of a lens system, which is an important step towards automatic design with artificial intelligence.

Adaptive mechanical-wetting lens actuated by ferrofluids

Science.gov (United States)

Cheng, Hui-Chuan; Xu, Su; Liu, Yifan; Levi, Shoshana; Wu, Shin-Tson

2011-04-01

We report an adaptive mechanical-wetting lens actuated by ferrofluids. The ferrofluids works like a piston to pump liquids in and out from the lens chamber, which in turn reshapes the lens curvature and changes the focal length. Both positive and negative lenses are demonstrated experimentally. The ferrofluid-actuated mechanical-wetting lens exhibits some attractive features, such as high resolution, fast response time, low power consumption, simple structure and electronic control, weak gravity effect, and low cost. Its potential applications in medical imaging, surveillance, and commercial electronics are foreseeable.

A Class I UV-Blocking (senofilcon A) Soft Contact Lens Prevents UVA-induced Yellow Fluorescence and NADH loss in the Rabbit Lens Nucleus in vivo

Science.gov (United States)

Giblin, Frank J.; Lin, Li-Ren; Simpanya, Mukoma F.; Leverenz, Victor R.; Fick, Catherine E.

2012-01-01

�-crystallin after the in vivo UVA exposure. It is concluded that UVA-induced loss of free NADH (which fluoresces blue) may have allowed the natural yellow fluorescence of λ-crystallin and other proteins in the lens nucleus to become visible. Increased fluorescence exhibited by UVA-exposed λ-crystallin may have been the result of a UVA-induced change in the conformation of the protein occurring during the initial UVA-exposure in vivo. The results demonstrate the greater susceptibility of the lens nucleus to UVA-induced stress, and may relate to the formation of human nuclear cataract. The senofilcon A contact lens was shown to be beneficial in protecting the rabbit lens against effects of UVA light, including changes in fluorescence, increased yellowing and loss of pyridine nucleotides. PMID:22766154

Submicron hollow spot generation by solid immersion lens and structured illumination

International Nuclear Information System (INIS)

Kim, M-S; Scharf, T; Herzig, H P; Assafrao, A C; Wachters, A J H; Pereira, S F; Urbach, H P; Brun, M; Olivier, S; Nicoletti, S

2012-01-01

We report on the experimental and numerical demonstration of immersed submicron-size hollow focused spots, generated by structuring the polarization state of an incident light beam impinging on a micro-size solid immersion lens (μ-SIL) made of SiO 2 . Such structured focal spots are characterized by a doughnut-shaped intensity distribution, whose central dark region is of great interest for optical trapping of nano-size particles, super-resolution microscopy and lithography. In this work, we have used a high-resolution interference microscopy technique to measure the structured immersed focal spots, whose dimensions were found to be significantly reduced due to the immersion effect of the μ-SIL. In particular, a reduction of 37% of the dark central region was verified. The measurements were compared with a rigorous finite element method model for the μ-SIL, revealing excellent agreement between them. (paper)

Heterologous expression and solution structure of defensin from lentil Lens culinaris

International Nuclear Information System (INIS)

Shenkarev, Zakhar O.; Gizatullina, Albina K.; Finkina, Ekaterina I.; Alekseeva, Ekaterina A.; Balandin, Sergey V.; Mineev, Konstantin S.; Arseniev, Alexander S.; Ovchinnikova, Tatiana V.

2014-01-01

Highlights: • Lentil defensin Lc-def and its 15 N-labeled analog were overexpressed in E. coli. • Lc-def is active against fungi, but does not inhibit growth of G+ and G− bacteria. • Lc-def spatial structure involves triple-stranded β-sheet and α-helix (CSαβ motif). • Lc-def is able to bind to anionic lipid vesicles under low-salt conditions. • NMR data revealed significant μs–ms mobility in the loops 1 and 3 of Lc-def. - Abstract: A new defensin Lc-def, isolated from germinated seeds of the lentil Lens culinaris, has molecular mass 5440.4 Da and consists of 47 amino acid residues. Lc-def and its 15 N-labeled analog were overexpressed in Escherichia coli. Antimicrobial activity of the recombinant protein was examined, and its spatial structure, dynamics, and interaction with lipid vesicles were studied by NMR spectroscopy. It was shown that Lc-def is active against fungi, but does not inhibit the growth of Gram-positive and Gram-negative bacteria. The peptide is monomeric in aqueous solution and contains one α-helix and triple-stranded β-sheet, which form cysteine-stabilized αβ motif (CSαβ) previously found in other plant defensins. The sterically neighboring loop1 and loop3 protrude from the defensin core and demonstrate significant mobility on the μs–ms timescale. Lc-def does not bind to the zwitterionic lipid (POPC) vesicles but interacts with the partially anionic (POPC/DOPG, 7:3) membranes under low-salt conditions. The Lc-def antifungal activity might be mediated through electrostatic interaction with anionic lipid components of fungal membranes

Heterologous expression and solution structure of defensin from lentil Lens culinaris

Energy Technology Data Exchange (ETDEWEB)

Shenkarev, Zakhar O. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow (Russian Federation); Gizatullina, Albina K. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700 Dolgoprudny, Moscow Region (Russian Federation); Finkina, Ekaterina I.; Alekseeva, Ekaterina A.; Balandin, Sergey V.; Mineev, Konstantin S. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow (Russian Federation); Arseniev, Alexander S. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700 Dolgoprudny, Moscow Region (Russian Federation); Ovchinnikova, Tatiana V., E-mail: ovch@ibch.ru [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700 Dolgoprudny, Moscow Region (Russian Federation)

2014-08-22

Highlights: • Lentil defensin Lc-def and its {sup 15}N-labeled analog were overexpressed in E. coli. • Lc-def is active against fungi, but does not inhibit growth of G+ and G− bacteria. • Lc-def spatial structure involves triple-stranded β-sheet and α-helix (CSαβ motif). • Lc-def is able to bind to anionic lipid vesicles under low-salt conditions. • NMR data revealed significant μs–ms mobility in the loops 1 and 3 of Lc-def. - Abstract: A new defensin Lc-def, isolated from germinated seeds of the lentil Lens culinaris, has molecular mass 5440.4 Da and consists of 47 amino acid residues. Lc-def and its {sup 15}N-labeled analog were overexpressed in Escherichia coli. Antimicrobial activity of the recombinant protein was examined, and its spatial structure, dynamics, and interaction with lipid vesicles were studied by NMR spectroscopy. It was shown that Lc-def is active against fungi, but does not inhibit the growth of Gram-positive and Gram-negative bacteria. The peptide is monomeric in aqueous solution and contains one α-helix and triple-stranded β-sheet, which form cysteine-stabilized αβ motif (CSαβ) previously found in other plant defensins. The sterically neighboring loop1 and loop3 protrude from the defensin core and demonstrate significant mobility on the μs–ms timescale. Lc-def does not bind to the zwitterionic lipid (POPC) vesicles but interacts with the partially anionic (POPC/DOPG, 7:3) membranes under low-salt conditions. The Lc-def antifungal activity might be mediated through electrostatic interaction with anionic lipid components of fungal membranes.

KCC isoforms in a human lens epithelial cell line (B3) and lens tissue extracts.

Science.gov (United States)

Misri, Sandeep; Chimote, Ameet A; Adragna, Norma C; Warwar, Ronald; Brown, Thomas L; Lauf, Peter K

2006-11-01

We recently reported potassium-chloride cotransporter activity in human lens epithelial B3 (HLE-B3) cells. The purpose of the present study was to demonstrate in these cells as well as in human lens tissue the potassium-chloride cotransport (KCC) isoforms by reverse transcriptase-polymerase chain reaction (RT-PCR), Western blotting and immunofluorescence microscopy. Of the four KCC genes known to encode the respective proteins and their spliced variants, RT-PCR with both rat and human primers revealed the predicted cDNA fragments of KCC1, KCC3a, KCC3b, and KCC4 but not KCC2 in both HLE-B3 cells and in human lens tissue extracts from cataractous patients. Polyclonal rabbit (rb) anti-rat (rt) and anti-human (hm) antibodies against rtKCC1 and hmKCC3, respectively, and a commercially available rb-anti-mouse (ms) KCC4 antibody were used. Rb anti-rtKCC1-ECL3 [against epitopes within the large extracellular loop 3 (ECL3)] revealed a 150kDa band in HLE-B3 cells consistent with the known molecular weight of KCC1. Rb anti-hmKCC3-ECL3 yielded three bands of 150, 122 and 105kDa, evidence for the presence of KCC3a, KCC3b and possibly KCC3c isoforms. The 122 and 112kDa bands were also demonstrated by rb anti-hmKCC3-CTD [the C-terminal domain (CTD)]. Rb anti-msKCC4 antibody only showed a 100kDa band in HLE-B3 cells. In the human lens tissues, a 115kDa protein was detected with rb anti-rtKCC1-ECL3 and a 100kDa band with rb anti-msKCC4, however, no bands with rb anti-hmKCC3-ECL3 or rb anti-hmKCC3-CTD. Fluorescence microscopy revealed immunocytochemical cytoplasmic and membrane labeling of HLE-B3 cells with anti-KCC1, -KCC3 (laser confocal microscopy) and -KCC4 antibodies and a Cy3-tagged secondary antibody. Hence HLE-B3 cells expressed proteins of the KCC1, KCC3a, b, and KCC4 isoforms, whereas surgically removed cataractous lens tissue expressed only those of KCC1 and KCC4.

Design of LED projector based on gradient-index lens

Science.gov (United States)

Qian, Liyong; Zhu, Xiangbing; Cui, Haitian; Wang, Yuanhang

2018-01-01

In this study, a new type of projector light path is designed to eliminate the deficits of existing projection systems, such as complex structure and low collection efficiency. Using a three-color LED array as the lighting source, by means of the special optical properties of a gradient-index lens, the complex structure of the traditional projector is simplified. Traditional components, such as the color wheel, relay lens, and mirror, become unnecessary. In this way, traditional problems, such as low utilization of light energy and loss of light energy, are solved. With the help of Zemax software, the projection lens is optimized. The optimized projection lens, LED, gradient-index lens, and digital micromirror device are imported into Tracepro. The ray tracing results show that both the utilization of light energy and the uniformity are improved significantly.

MP20, the second most abundant lens membrane protein and member of the tetraspanin superfamily, joins the list of ligands of galectin-3

Directory of Open Access Journals (Sweden)

Donaldson Paul J

2001-08-01

Full Text Available Abstract Background Although MP20 is the second most highly expressed membrane protein in the lens its function remains an enigma. Putative functions for MP20 have recently been inferred from its assignment to the tetraspanin superfamily of integral membrane proteins. Members of this family have been shown to be involved in cellular proliferation, differentiation, migration, and adhesion. In this study, we show that MP20 associates with galectin-3, a known adhesion modulator. Results MP20 and galectin-3 co-localized in selected areas of the lens fiber cell plasma membrane. Individually, these proteins purified with apparent molecular masses of 60 kDa and 22 kDa, respectively. A 104 kDa complex was formed in vitro upon mixing the purified proteins. A 102 kDa complex of MP20 and galectin-3 could also be isolated from detergent-solubilized native fiber cell membranes. Binding between MP20 and galectin-3 was disrupted by lactose suggesting the lectin site was involved in the interaction. Conclusions MP20 adds to a growing list of ligands of galectin-3 and appears to be the first representative of the tetraspanin superfamily identified to possess this specificity.

Dating the time of birth: A radiocarbon calibration curve for human eye-lens crystallines

DEFF Research Database (Denmark)

Kjeldsen, Henrik; Heinemeier, Jan; Heegaard, Steffen

2010-01-01

Radiocarbon bomb-pulse dating has been used to measure the formation age of human eye-lens crystallines. Lens crystallines are special proteins in the eye-lens that consist of virtually inert tissue. The experimental data show that the radiocarbon ages to a large extent reflect the time of birth...

Crystalline lens and refractive development.

Science.gov (United States)

Iribarren, Rafael

2015-07-01

Individual refractive errors usually change along lifespan. Most children are hyperopic in early life. This hyperopia is usually lost during growth years, leading to emmetropia in adults, but myopia also develops in children during school years or during early adult life. Those subjects who remain emmetropic are prone to have hyperopic shifts in middle life. And even later, at older ages, myopic shifts are developed with nuclear cataract. The eye grows from 15 mm in premature newborns to approximately 24 mm in early adult years, but, in most cases, refractions are maintained stable in a clustered distribution. This growth in axial length would represent a refractive change of more than 40 diopters, which is compensated by changes in corneal and lens powers. The process which maintains the balance between the ocular components of refraction during growth is still under study. As the lens power cannot be measured in vivo, but can only be calculated based on the other ocular components, there have not been many studies of lens power in humans. Yet, recent studies have confirmed that the lens loses power during growth in children, and that hyperopic and myopic shifts in adulthood may be also produced by changes in the lens. These studies in children and adults give a picture of the changing power of the lens along lifespan. Other recent studies about the growth of the lens and the complexity of its internal structure give clues about how these changes in lens power are produced along life. Copyright © 2015 Elsevier Ltd. All rights reserved.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

The Role of Type IV Collagen in Developing Lens in Mouse Fetuses

Directory of Open Access Journals (Sweden)

Mehdi Jalali

2009-09-01

Full Text Available Objective(sExtracellular matrix (ECM and basement membrane (BM play important roles in many developmental processes during development and after birth. Among the components of the BM, collagen fibers specially type IV are the most important parts. The aim of this study was to determine the time when collagen type IV appears in the BM of lens structure during mouse embryonic development.Materials and MethodsIn this experimental study, 22 female Balb/C mice were randomly selected and were kept under normal condition, finding vaginal plug was assumed as day zero of pregnancy. From embryonic day 10 to 20, all specimens were sacrificed by cervical dislocation and their heads were fixed, serially sectioned and immunohistochemistry study for tracing collagen type IV in lens were carried out.ResultsOur data revealed that collagen type IV appeared at the early stage of gestation day 12 in BM of anterior epithelial lens cells and the amount of this protein gradually increased until days 15-17 in ECM and posterior capsule epithelium. After this period, severe reaction was not observed in any part of the lens.ConclusionThese findings establish the important role of collagen IV in developing optic cup and any changes during critical period of pregnancy may be result in severe visual system defect

Lens stem cells may reside outside the lens capsule: an hypothesis

Directory of Open Access Journals (Sweden)

Meyer Rita A

2007-06-01

Full Text Available Abstract In this paper, we consider the ocular lens in the context of contemporary developments in biological ideas. We attempt to reconcile lens biology with stem cell concepts and a dearth of lens tumors. Historically, the lens has been viewed as a closed system, in which cells at the periphery of the lens epithelium differentiate into fiber cells. Theoretical considerations led us to question whether the intracapsular lens is indeed self-contained. Since stem cells generate tumors and the lens does not naturally develop tumors, we reasoned that lens stem cells may not be present within the capsule. We hypothesize that lens stem cells reside outside the lens capsule, in the nearby ciliary body. Our ideas challenge the existing lens biology paradigm. We begin our discussion with lens background information, in order to describe our lens stem cell hypothesis in the context of published data. Then we present the ciliary body as a possible source for lens stem cells, and conclude by comparing the ocular lens with the corneal epithelium.

Birc7: A Late Fiber Gene of the Crystalline Lens.

Science.gov (United States)

De Maria, Alicia; Bassnett, Steven

2015-07-01

A distinct subset of genes, so-called "late fiber genes," is expressed in cells bordering the central, organelle-free zone (OFZ) of the lens. The purpose of this study was to identify additional members of this group. Fiber cells were harvested from various layers of the lens by laser micro-dissection and subjected to microarray, in situ hybridization, and Western blot analysis. Expression of Livin, a member of the inhibitor of apoptosis protein (IAP) family encoded by Birc7, was strongly upregulated in deep cortical fiber cells. The depth-dependent distribution of Livin mRNA was confirmed by quantitative PCR and in situ hybridization. The onset of Livin expression coincided with loss of organelles from primary fiber cells. Livin expression peaked at 1 month but was sustained even in aged lenses. Antibodies raised against mouse Livin labeled multiple bands on immunoblots, reflecting progressive proteolysis of the parent molecule during differentiation. Mice harboring a floxed Birc7 allele were generated and used to conditionally delete Birc7 in lens. Lenses from knockout mice grew normally and retained their transparency, suggesting that Livin does not have an indispensable role in fiber cell differentiation. Birc7 is a late fiber gene of the mouse lens. In tumor cells, Livin acts as an antiapoptotic protein, but its function in the lens is enigmatic. Livin is a RING domain protein with putative E3 ubiquitin ligase activity. Its expression in cells bordering the OFZ is consistent with a role in organelle degradation, a process in which the ubiquitin proteasome pathway has been implicated previously.

α-Crystallin localizes to the leading edges of migrating lens epithelial cells

International Nuclear Information System (INIS)

Maddala, Rupalatha; Vasantha Rao, P.

2005-01-01

α-crystallin (αA and αB) is a major lens protein, which belongs to the small heat-shock family of proteins and binds to various cytoskeletal proteins including actin, vimentin and desmin. In this study, we investigated the cellular localization of αA and αB-crystallins in migrating epithelial cells isolated from porcine lens. Immunofluorescence localization and confocal imaging of αB-crystallin in confluent and in migrating subconfluent cell cultures revealed a distinct pattern of subcellular distribution. While αB-crystallin localization was predominantly cytoplasmic in confluent cultures, it was strongly localized to the leading edges of cell membrane or the lamellipodia in migrating cells. In accordance with this pattern, we found abundant levels of αB-crystallin in membrane fractions compared to cytosolic and nuclear fractions in migrating lens epithelial cells. αA-crystallin, which has 60% sequence identity to αB-crystallin, also exhibited a distribution profile localizing to the leading edge of the cell membrane in migrating lens epithelial cells. Localization of αB-crystallin to the lamellipodia appears to be dependent on phosphorylation of residue serine-59. An inhibitor of p38 MAP kinase (SB202190), but not the ERK kinase inhibitor PD98059, was found to diminish localization of αB-crystallin to the lamellipodia, and this effect was found to be associated with reduced levels of Serine-59 phosphorylated αB-crystallin in SB202190-treated migrating lens epithelial cells. αB-crystallin localization to the lamellipodia was also altered by the treatment with RGD (Arg-Ala-Asp) peptide, dominant negative N17 Rac1 GTPase, cytochalasin D and Src kinase inhibitor (PP2), but not by the Rho kinase inhibitor Y-27632 or the myosin II inhibitor, blebbistatin. Additionally, in migrating lens epithelial cells, αB-crystallin exhibited a clear co-localization with the actin meshwork, β-catenin, WAVE-1, a promoter of actin nucleation, Abi-2, a component of WAVE

Eye lens membrane junctional microdomains: a comparison between healthy and pathological cases

Energy Technology Data Exchange (ETDEWEB)

Buzhynskyy, Nikolay; Scheuring, Simon [Institut Curie, Equipe Inserm Avenir, UMR168-CNRS, 26 Rue d' Ulm, 75248 Paris Cedex 05 (France); Sens, Pierre [ESPCI, CNRS-UMR 7083, 75231 Paris (France); Behar-Cohen, Francine, E-mail: simon.scheuring@curie.fr [UMRS Inserm 872, Universite Paris Descartes, Centre de Recherches des Cordeliers, 15 rue de l' Ecole de Medecine, 75270 Paris Cedex 06 (France)

2011-08-15

The eye lens is a transparent tissue constituted of tightly packed fiber cells. To maintain homeostasis and transparency of the lens, the circulation of water, ions and metabolites is required. Junctional microdomains connect the lens cells and ensure both tight cell-to-cell adhesion and intercellular flow of fluids through a microcirculation system. Here, we overview membrane morphology and tissue functional requirements of the mammalian lens. Atomic force microscopy (AFM) has opened up the possibility of visualizing the junctional microdomains at unprecedented submolecular resolution, revealing the supramolecular assembly of lens-specific aquaporin-0 (AQP0) and connexins (Cx). We compare the membrane protein assembly in healthy lenses with senile and diabetes-II cataract cases and novel data of the lens membranes from a congenital cataract. In the healthy case, AQP0s form characteristic square arrays confined by connexons. In the cases of senile and diabetes-II cataract patients, connexons were degraded, leading to malformation of AQP0 arrays and breakdown of the microcirculation system. In the congenital cataract, connexons are present, indicating probable non-membranous grounds for lens opacification. Further, we discuss the energetic aspects of the membrane organization in junctional microdomains. The AFM hence becomes a biomedical nano-imaging tool for the analysis of single-membrane protein supramolecular association in healthy and pathological membranes.

Eye lens membrane junctional microdomains: a comparison between healthy and pathological cases

Science.gov (United States)

Buzhynskyy, Nikolay; Sens, Pierre; Behar-Cohen, Francine; Scheuring, Simon

2011-08-01

The eye lens is a transparent tissue constituted of tightly packed fiber cells. To maintain homeostasis and transparency of the lens, the circulation of water, ions and metabolites is required. Junctional microdomains connect the lens cells and ensure both tight cell-to-cell adhesion and intercellular flow of fluids through a microcirculation system. Here, we overview membrane morphology and tissue functional requirements of the mammalian lens. Atomic force microscopy (AFM) has opened up the possibility of visualizing the junctional microdomains at unprecedented submolecular resolution, revealing the supramolecular assembly of lens-specific aquaporin-0 (AQP0) and connexins (Cx). We compare the membrane protein assembly in healthy lenses with senile and diabetes-II cataract cases and novel data of the lens membranes from a congenital cataract. In the healthy case, AQP0s form characteristic square arrays confined by connexons. In the cases of senile and diabetes-II cataract patients, connexons were degraded, leading to malformation of AQP0 arrays and breakdown of the microcirculation system. In the congenital cataract, connexons are present, indicating probable non-membranous grounds for lens opacification. Further, we discuss the energetic aspects of the membrane organization in junctional microdomains. The AFM hence becomes a biomedical nano-imaging tool for the analysis of single-membrane protein supramolecular association in healthy and pathological membranes.

A Class I UV-blocking (senofilcon A) soft contact lens prevents UVA-induced yellow fluorescence and NADH loss in the rabbit lens nucleus in vivo.

Science.gov (United States)

Giblin, Frank J; Lin, Li-Ren; Simpanya, Mukoma F; Leverenz, Victor R; Fick, Catherine E

2012-09-01

�-crystallin after the in vivo UVA exposure. It is concluded that UVA-induced loss of free NADH (which fluoresces blue) may have allowed the natural yellow fluorescence of λ-crystallin and other proteins in the lens nucleus to become visible. Increased fluorescence exhibited by UVA-exposed λ-crystallin may have been the result of a UVA-induced change in the conformation of the protein occurring during the initial UVA-exposure in vivo. The results demonstrate the greater susceptibility of the lens nucleus to UVA-induced stress, and may relate to the formation of human nuclear cataract. The senofilcon A contact lens was shown to be beneficial in protecting the rabbit lens against effects of UVA light, including changes in fluorescence, increased yellowing and loss of pyridine nucleotides. Copyright © 2012 Elsevier Ltd. All rights reserved.

Notes on electropherograms of eye-lens, muscle proteins and zymograms of muscle esterases of fish collected during the first Brazilian expedition to the Antarctica

Directory of Open Access Journals (Sweden)

Van Ngan Phan

1985-01-01

Full Text Available A preliminary study was carried out on electropherograms of eye-lens, muscle proteins and zymograms of muscle esterases of ten Notothenia larseni, six Notothenia nudifrons and one lanternfish, Electrona antarctica. The fish were collected by the R/V "Prof. W. Besnard" of the Institute of Oceanography, University of São Paulo, during the First Brazilian Expedition to Antarctica. Eye-lens proteins were analysed on cellulose acetate membrane, muscle proteins and esterases on gel of polyaorylamide. Eye-lens proteins showed three types of electropherograms for N. larseni, and two types for N. nudifrons. One of the electropherograms of N. larseni can be readily distinguished from those of N. nudifrons. Electropherograms of muscle proteins of N. larseni and N. nudifrons are very similar and, consist of sixteen to seventeen fractions. Electropherograms of muscle proteins of N. larseni are severely affected by the conservation of the extracts overnight under -20ºC. All N. nudifrons were of the same zymograms of esterases while those of N. larseni varied. Electropherograms of eye-lens and muscle proteins as well as zymograms of esterases of the lanternfish are different from those of nototheniids.Foi realizado um estudo preliminar sobre eletroferogramas de proteínas de cristalino e de músculo esquelético, e zimogramas de esterases de músculo esquelético de dez Notothenia larseni, seis Notothenia nudifrons e de um peixe-lanterna, Electrona antarctica. Os peixes foram coletados pelo N/Oc. "Prof. W. Besnard" do Instituto Oceanográfico da Universidade de São Paulo durante a I Expedição Brasileira à Antártica. As proteinas do cristalino foram analisadas em membranas de acetato de celulose, enquanto que as proteínas e esterases do músculo esquelético, em gel de poliacrilamida. As proteínas do cristalino apresentam três tipos distintos de eletroferogramas para N. larseni, e dois para N. nudifrons. Um dos eletroferogramas de N. larseni, pode ser

Non-invasive bleaching of the human lens by femtosecond laser photolysis

DEFF Research Database (Denmark)

Kessel, L.; Eskildsen, Lars; Poel, Mike van der

2010-01-01

. Reducing blindness from cataract requires solutions that can be applied outside operating theatres. Cataract is a protein conformational disease characterized by accumulation of light absorbing, fluorescent and scattering protein aggregates. The aim of the study was to investigate whether these compounds...... by a non-invasive procedure based on femtosecond laser photolysis. Cataract is a disease associated with old age. At the current technological stage, lens aging is delayed but with a treatment covering the entire lens volume complete optical rejuvenation is expected. Thus, femtosecond photolysis has...

cAMP-dependent phosphorylation of bovine lens alpha-crystallin

International Nuclear Information System (INIS)

Spector, A.; Chiesa, R.; Sredy, J.; Garner, W.

1985-01-01

This communication reports that the A1 and B1 chains of bovine lens alpha-crystallin are phosphorylated. The conclusion is based on the following evidence: (i) When soluble preparations from lens cortex are incubated with [gamma- 32 P]ATP, a cAMP-dependent labeling of a high molecular weight protein is obtained. (ii) After NaDodSO 4 /PAGE, the label is found in two bands with Mr 22,000 and 20,000, corresponding to the B and A chains of alpha-crystallin, respectively. (iii) Isoelectric focusing indicates that the radioactivity is almost exclusively in bands with pI values of 5.58 and 6.70, corresponding to the A1 and B1 chains, respectively. (iv) Similar results are obtained in experiments of [ 32 P]orthophosphate incorporation in lens organ culture. (v) Analyses of the digested protein indicate the label is exclusively in phosphoserine. (vi) 31 P NMR analyses of native, proteolytically digested, and urea-treated alpha-crystallin gives a chemical shift of 4.6 ppm relative to 85% H 3 PO 4 at pH 7.4, suggesting that the phosphate is covalently bound to a serine in the protein. An abundance of approximately one phosphate per four or five monomer units was found. (vii) Similar results were obtained by chemical analyses of independently prepared alpha-crystallin samples. The results are consistent with the view that the A1 and B1 chains arise as result of the phosphorylation of directly synthesized A2 and B2 polypeptides. It is suggested that this metabolically controlled phosphorylation may be associated with the terminal differentiation of the lens epithelial cell and the intracellular organization of the lens fiber cell

The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development.

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Archana D Siddam

2018-03-01

Full Text Available Opacification of the ocular lens, termed cataract, is a common cause of blindness. To become transparent, lens fiber cells undergo degradation of their organelles, including their nuclei, presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing toward compromised transcriptional potential? We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. Celf1-targeted knockout mice and celf1-knockdown zebrafish and Xenopus morphants have severe eye defects/cataract. Celf1 spatiotemporally down-regulates the cyclin-dependent kinase (Cdk inhibitor p27Kip1 by interacting with its 5' UTR and mediating translation inhibition. Celf1 deficiency causes ectopic up-regulation of p21Cip1. Further, Celf1 directly binds to the mRNA of the nuclease Dnase2b to maintain its high levels. Together these events are necessary for Cdk1-mediated lamin A/C phosphorylation to initiate nuclear envelope breakdown and DNA degradation in fiber cells. Moreover, Celf1 controls alternative splicing of the membrane-organization factor beta-spectrin and regulates F-actin-crosslinking factor Actn2 mRNA levels, thereby controlling fiber cell morphology. Thus, we illustrate new Celf1-regulated molecular mechanisms in lens development, suggesting that post-transcriptional regulatory RNA-binding proteins have evolved conserved functions to control vertebrate oculogenesis.

Azimuthally anisotropic hydride lens structures in Zircaloy 4 nuclear fuel cladding: High-resolution neutron radiography imaging and BISON finite element analysis

Science.gov (United States)

Lin, Jun-Li; Zhong, Weicheng; Bilheux, Hassina Z.; Heuser, Brent J.

2017-12-01

High-resolution neutron radiography has been used to image bulk circumferential hydride lens particles in unirradiated Zircaloy 4 tubing cross section specimens. Zircaloy 4 is a common light water nuclear reactor (LWR) fuel cladding; hydrogen pickup, hydride formation, and the concomitant effect on the mechanical response are important for LWR applications. Ring cross section specimens with three hydrogen concentrations (460, 950, and 2830 parts per million by weight) and an as-received reference specimen were imaged. Azimuthally anisotropic hydride lens particles were observed at 950 and 2830 wppm. The BISON finite element analysis nuclear fuel performance code was used to model the system elastic response induced by hydride volumetric dilatation. The compressive hoop stress within the lens structure becomes azimuthally anisotropic at high hydrogen concentrations or high hydride phase fraction. This compressive stress anisotropy matches the observed lens anisotropy, implicating the effect of stress on hydride formation as the cause of the observed lens azimuthal asymmetry. The cause and effect relation between compressive stress and hydride lens anisotropy represents an indirect validation of a key BISON output, the evolved hoop stress associated with hydride formation.

Myo/Nog cells: targets for preventing the accumulation of skeletal muscle-like cells in the human lens.

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Jacquelyn Gerhart

Full Text Available Posterior capsule opacification (PCO is a vision impairing condition that arises in some patients following cataract surgery. The fibrotic form of PCO is caused by myofibroblasts that may emerge in the lens years after surgery. In the chick embryo lens, myofibroblasts are derived from Myo/Nog cells that are identified by their expression of the skeletal muscle specific transcription factor MyoD, the bone morphogenetic protein inhibitor Noggin, and the epitope recognized by the G8 monoclonal antibody. The goal of this study was to test the hypothesis that depletion of Myo/Nog cells will prevent the accumulation of myofibroblasts in human lens tissue. Myo/Nog cells were present in anterior, equatorial and bow regions of the human lens, cornea and ciliary processes. In anterior lens tissue removed by capsulorhexis, Myo/Nog cells had synthesized myofibroblast and skeletal muscle proteins, including vimentin, MyoD and sarcomeric myosin. Alpha smooth muscle actin (α-SMA was detected in a subpopulation of Myo/Nog cells. Areas of the capsule denuded of epithelial cells were surrounded by Myo/Nog cells. Some of these cell free areas contained a wrinkle in the capsule. Depletion of Myo/Nog cells eliminated cells expressing skeletal muscle proteins in 5-day cultures but did not affect cells immunoreactive for beaded filament proteins that accumulate in differentiating lens epithelial cells. Transforming growth factor-betas 1 and 2 that mediate an epithelial-mesenchymal transition, did not induce the expression of skeletal muscle proteins in lens cells following Myo/Nog cell depletion. This study demonstrates that Myo/Nog cells in anterior lens tissue removed from cataract patients have undergone a partial differentiation to skeletal muscle. Myo/Nog cells appear to be the source of skeletal muscle-like cells in explants of human lens tissue. Targeting Myo/Nog cells with the G8 antibody during cataract surgery may reduce the incidence of PCO.

Different alpha crystallin expression in human age-related and congenital cataract lens epithelium.

Science.gov (United States)

Yang, Jing; Zhou, Sheng; Guo, Minfei; Li, Yuting; Gu, Jianjun

2016-05-28

The purpose of this study was to investigate the different expressions of αA-crystallin and αB-crystallin in human lens epithelium of age-related and congenital cataracts. The central part of the human anterior lens capsule approximately 5 mm in diameter together with the adhering epithelial cells, were harvested and processed within 6 hours after cataract surgery from age-related and congenital cataract patients or from normal eyes of fresh cadavers. The mRNA and soluble protein levels of αA-crystallin and αB-crystallin in the human lens epithelium were detected by real-time PCR and western blots, respectively. The mRNA and soluble protein expressions of αA-crystallin and αB-crystallin in the lens epithelium were both reduced in age-related and congenital cataract groups when compared with the normal control group. However, the degree of α-crystallin loss in the lens epithelium was highly correlated with different cataract types. The α-crystallin expression of the lens epithelium was greatly reduced in the congenital cataract group but only moderately decreased in the age-related cataract group. The reduction of αA-crystallin soluble protein levels in the congenital cataract group was approximately 2.4 fold decrease compared with that of the age-related cataract group, while an mRNA fold change of 1.67 decrease was observed for the age-related cataract group. Similarly, the reduction of soluble protein levels of αB-crystallin in the congenital cataract group was approximately a 1.57 fold change compared with that of the age-related cataract group. A 1.75 fold change for mRNA levels compared with that of the age-related cataract group was observed. The results suggest that the differential loss of α-crystallin in the human lens epithelium could be associated with the different mechanisms of cataractogenesis in age-related versus congenital cataracts, subsequently resulting in different clinical presentations.

Effects of Coupling Lens on Optical Refrigeration of Semiconductors

International Nuclear Information System (INIS)

Kai, Ding; Yi-Ping, Zeng

2008-01-01

Optical refrigeration of semiconductors is encountering efficiency difficulties caused by nonradiative recombination and luminescence trapping. A commonly used approach for enhancing luminescence efficiency of a semiconductor device is coupling a lens with the device. We quantitatively study the effects of a coupling lens on optical refrigeration based on rate equations and photon recycling, and calculated cooling efficiencies of different coupling mechanisms and of different lens materials. A GaAs/GaInP heterostructure coupled with a homo-epitaxial GaInP hemispherical lens is recommended. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

D-aspartic acid in aged mouse skin and lens

International Nuclear Information System (INIS)

Fujii, Noriko; Muraoka, Shiro; Harada, Kaoru; Tamanoi, Itsuro; Joshima, Hisamasa; Kashima, Masatoshi.

1987-01-01

D-aspartic acid (D-Asp) was detected in the skin and lens from naturally aged mice. An analysis of the amino acid composition indicated that D-Asp did not derive from collagen. An immunological analysis using Oucterlony's agar diffusion method also confirmed that the protein containing D-Asp was not a serum protein. The process producing D-Asp is regarded as one other than racemization because the life span of mice is not long enough to permit D-Asp by racemization. Continuous low-dose-rate gamma-irradiation (37R per day) for 102 to 112 days did not increase significantly the amount of D-Asp in skin and lens of mice. (author)

Lens-Aided Multi-Angle Spectroscopy (LAMAS) Reveals Small-Scale Outflow Structure in Quasars

Science.gov (United States)

Green, Paul J.

2006-06-01

Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. Here we advance a novel third hypothesis: some spectral differences are due to small line-of-sight differences through quasar disk wind outflows. In particular, we propose that variable spectral differences seen only in component A of the widest separation lens SDSS J1004+4112 are due to differential absorption along the sight lines. The absorber properties required by this hypothesis are akin to known broad absorption line (BAL) outflows but must have a broader, smoother velocity profile. We interpret the observed C IV emission-line variability as further evidence for spatial fine structure transverse to the line of sight. Since outflows are likely to be rotating, such absorber fine structure can consistently explain some of the UV and X-ray variability seen in AGNs. The implications are many: (1) Spectroscopic differences in other lensed objects may be due to this ``lens-aided multi-angle spectroscopy'' (LAMAS). (2) Outflows have fine structure on size scales of arcseconds, as seen from the nucleus. (3) Assuming either broad absorption line region sizes proposed in recent wind models, or typically assumed continuum emission region sizes, LAMAS and/or variability provide broadly consistent absorber size scale estimates of ~1015 cm. (4) Very broad smooth absorption may be ubiquitous in quasar spectra, even when no obvious troughs are seen.

Oligomeric protein structure networks: insights into protein-protein interactions

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Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Modularity in protein structures: study on all-alpha proteins.

Science.gov (United States)

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

A Correlation of Thin Lens Approximation to Thick Lens Design by Using Coddington Factors in Lens Design and Manufacturing

OpenAIRE

FARSAKOĞLU, Ö. Faruk

2014-01-01

The effect of Coddington factors on aberration functions has been analysed using thin lens approximation. Minimizing spherical aberrations of singlet lenses using Coddington factors in lens design depending on lens manufacturing is discussed. Notation of lens test plate pairs used in lens manufacturing is also presented in terms of Coddington shape factors.

Mapping monomeric threading to protein-protein structure prediction.

Science.gov (United States)

Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2013-03-25

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

Nuclear magnetic resonance studies of lens transparency

International Nuclear Information System (INIS)

Beaulieu, C.F.

1989-01-01

Transparency of normal lens cytoplasm and loss of transparency in cataract were studied by nuclear magnetic resonance (NMR) methods. Phosphorus ( 31 P) NMR spectroscopy was used to measure the 31 P constituents and pH of calf lens cortical and nuclear homogenates and intact lenses as a function of time after lens enucleation and in opacification produced by calcium. Transparency was measured with laser spectroscopy. Despite complete loss of adenosine triphosphate (ATP) within 18 hrs of enucleation, the homogenates and lenses remained 100% transparent. Additions of calcium to ATP-depleted cortical homogenates produced opacification as well as concentration-dependent changes in inorganic phosphate, sugar phosphates, glycerol phosphorylcholine and pH. 1 H relaxation measurements of lens water at 200 MHz proton Larmor frequency studied temperature-dependent phase separation of lens nuclear homogenates. Preliminary measurements of T 1 and T 2 with non-equilibrium temperature changes showed a change in the slope of the temperature dependence of T 1 and T 2 at the phase separation temperature. Subsequent studies with equilibrium temperature changes showed no effect of phase separation on T 1 or T 2 , consistent with the phase separation being a low-energy process. 1 H nuclear magnetic relaxation dispersion (NMRD) studies (measurements of the magnetic field dependence of the water proton 1/T 1 relaxation rates) were performed on (1) calf lens nuclear and cortical homogenates (2) chicken lens homogenates, (3) native and heat-denatured egg white and (4) pure proteins including bovine γ-II crystallin bovine serum albumin (BSA) and myoglobin. The NMRD profiles of all samples exhibited decreases in 1/T 1 with increasing magnetic field

Alzheimer's disease amyloid-beta links lens and brain pathology in Down syndrome.

Directory of Open Access Journals (Sweden)

Juliet A Moncaster

2010-05-01

Full Text Available Down syndrome (DS, trisomy 21 is the most common chromosomal disorder and the leading genetic cause of intellectual disability in humans. In DS, triplication of chromosome 21 invariably includes the APP gene (21q21 encoding the Alzheimer's disease (AD amyloid precursor protein (APP. Triplication of the APP gene accelerates APP expression leading to cerebral accumulation of APP-derived amyloid-beta peptides (Abeta, early-onset AD neuropathology, and age-dependent cognitive sequelae. The DS phenotype complex also includes distinctive early-onset cerulean cataracts of unknown etiology. Previously, we reported increased Abeta accumulation, co-localizing amyloid pathology, and disease-linked supranuclear cataracts in the ocular lenses of subjects with AD. Here, we investigate the hypothesis that related AD-linked Abeta pathology underlies the distinctive lens phenotype associated with DS. Ophthalmological examinations of DS subjects were correlated with phenotypic, histochemical, and biochemical analyses of lenses obtained from DS, AD, and normal control subjects. Evaluation of DS lenses revealed a characteristic pattern of supranuclear opacification accompanied by accelerated supranuclear Abeta accumulation, co-localizing amyloid pathology, and fiber cell cytoplasmic Abeta aggregates (approximately 5 to 50 nm identical to the lens pathology identified in AD. Peptide sequencing, immunoblot analysis, and ELISA confirmed the identity and increased accumulation of Abeta in DS lenses. Incubation of synthetic Abeta with human lens protein promoted protein aggregation, amyloid formation, and light scattering that recapitulated the molecular pathology and clinical features observed in DS lenses. These results establish the genetic etiology of the distinctive lens phenotype in DS and identify the molecular origin and pathogenic mechanism by which lens pathology is expressed in this common chromosomal disorder. Moreover, these findings confirm increased Abeta

The etiology of human age-related cataract. Proteins don't last forever.

Science.gov (United States)

Truscott, Roger J W; Friedrich, Michael G

2016-01-01

It is probable that the great majority of human cataract results from the spontaneous decomposition of long-lived macromolecules in the human lens. Breakdown/reaction of long-lived proteins is of primary importance and recent proteomic analysis has enabled the identification of the particular crystallins, and their exact sites of amino acid modification. Analysis of proteins from cataractous lenses revealed that there are sites on some structural proteins that show a consistently greater degree of deterioration than age-matched normal lenses. The most abundant posttranslational modification of aged lens proteins is racemization. Deamidation, truncation and crosslinking, each arising from the spontaneous breakdown of susceptible amino acids within proteins, are also present. Fundamental to an understanding of nuclear cataract etiology, it is proposed that once a certain degree of modification at key sites occurs, that protein-protein interactions are disrupted and lens opacification ensues. Since long-lived proteins are now recognized to be present in many other sites of the body, such as the brain, the information gleaned from detailed analyses of degraded proteins from aged lenses will apply more widely to other age-related human diseases. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease. Copyright © 2015 Elsevier B.V. All rights reserved.

Dating the time of birth: A radiocarbon calibration curve for human eye-lens crystallines

International Nuclear Information System (INIS)

Kjeldsen, Henrik; Heinemeier, Jan; Heegaard, Steffen; Jacobsen, Christina; Lynnerup, Niels

2010-01-01

Radiocarbon bomb-pulse dating has been used to measure the formation age of human eye-lens crystallines. Lens crystallines are special proteins in the eye-lens that consist of virtually inert tissue. The experimental data show that the radiocarbon ages to a large extent reflect the time of birth, in accordance with expectations. Moreover, it has been possible to develop an age model for the formation of the eye-lens crystallines. From this model a radiocarbon calibration curve for lens crystallines has been calculated. As a consequence, the time of birth of humans can be determined with an accuracy of a few years by radiocarbon dating.

Dating the time of birth: A radiocarbon calibration curve for human eye-lens crystallines

Energy Technology Data Exchange (ETDEWEB)

Kjeldsen, Henrik, E-mail: kjeldsen@phys.au.d [AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Aarhus (Denmark); Heinemeier, Jan [AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Aarhus (Denmark); Heegaard, Steffen [Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen (Denmark); Jacobsen, Christina; Lynnerup, Niels [Department of Forensic Medicine, University of Copenhagen, Copenhagen (Denmark)

2010-04-15

Radiocarbon bomb-pulse dating has been used to measure the formation age of human eye-lens crystallines. Lens crystallines are special proteins in the eye-lens that consist of virtually inert tissue. The experimental data show that the radiocarbon ages to a large extent reflect the time of birth, in accordance with expectations. Moreover, it has been possible to develop an age model for the formation of the eye-lens crystallines. From this model a radiocarbon calibration curve for lens crystallines has been calculated. As a consequence, the time of birth of humans can be determined with an accuracy of a few years by radiocarbon dating.

Immunohistochemical studies of lens crystallins in the dysgenetic lens (dyl) mutant mice

NARCIS (Netherlands)

Brahma, S.K.; Sanyal, S.

1984-01-01

The lens in the dyl mutant mice shows a persistent lens-ectodermal connection as well as degeneration and extrusion of lens materials after the initial differentiation of the fibres. Immunohistochemical investigation of the ontogeny of the lens crystallins in this developing mutant lens has been

Sharing of secondary electrons by in-lens and out-lens detector in low-voltage scanning electron microscope equipped with immersion lens.

Science.gov (United States)

Kumagai, Kazuhiro; Sekiguchi, Takashi

2009-03-01

To understand secondary electron (SE) image formation with in-lens and out-lens detector in low-voltage scanning electron microscopy (LV-SEM), we have evaluated SE signals of an in-lens and an out-lens detector in LV-SEM. From the energy distribution spectra of SEs with various boosting voltages of the immersion lens system, we revealed that the electrostatic field of the immersion lens mainly collects electrons with energy lower than 40eV, acting as a low-pass filter. This effect is also observed as a contrast change in LV-SEM images taken by in-lens and out-lens detectors.

Protein enriched pasta: structure and digestibility of its protein network.

Science.gov (United States)

Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

2016-02-01

Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

Structure-based barcoding of proteins.

Science.gov (United States)

Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

2014-01-01

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

Science.gov (United States)

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

KAUST Repository

Cui, Xuefeng

2016-06-15

Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

Tunable Focus Liquid Lens with Radial-Patterned Electrode

Directory of Open Access Journals (Sweden)

Miao Xu

2015-08-01

Full Text Available A dielectric liquid lens is prepared based on our previous work. By optimizing the device structure, the liquid lens presents a converging focus with good resolution and changes its focal length over a broad range with a low driving voltage. For a liquid lens with ~2.3 mm diameter in the relaxed state, it can resolve ~40 lp/mm. The resolution does not degrade during focus change. Its focal length can be varied from ~12 to ~5 mm when the applied voltage is changed from 0 to 28 Vrms. The response time of one cycle is ~2.5 s. Our liquid lens, with a low driving voltage for a large dynamic range, has potential applications in imaging, biometrics, optoelectronic, and lab-on-chip devices.

Wide-field schematic eye models with gradient-index lens.

Science.gov (United States)

Goncharov, Alexander V; Dainty, Chris

2007-08-01

We propose a wide-field schematic eye model, which provides a more realistic description of the optical system of the eye in relation to its anatomical structure. The wide-field model incorporates a gradient-index (GRIN) lens, which enables it to fulfill properties of two well-known schematic eye models, namely, Navarro's model for off-axis aberrations and Thibos's chromatic on-axis model (the Indiana eye). These two models are based on extensive experimental data, which makes the derived wide-field eye model also consistent with that data. A mathematical method to construct a GRIN lens with its iso-indicial contours following the optical surfaces of given asphericity is presented. The efficiency of the method is demonstrated with three variants related to different age groups. The role of the GRIN structure in relation to the lens paradox is analyzed. The wide-field model with a GRIN lens can be used as a starting design for the eye inverse problem, i.e., reconstructing the optical structure of the eye from off-axis wavefront measurements. Anatomically more accurate age-dependent optical models of the eye could ultimately help an optical designer to improve wide-field retinal imaging.

Vortexlike Power Flow at the Interfaces of Metamaterial Lens

Directory of Open Access Journals (Sweden)

K. Fang

2012-10-01

Full Text Available The metamaterial lens with DPS/DNS/DPS structure has been realized by using the two-dimensional (2D isotropic transmission line approach. We studied the vortexlike power flow at the interfaces of metamaterial lens and validated by the finite-difference time-domain (FDTD simulator. The computational results showing its different conditions near DPS/DNS and other kinds of interfaces are obtained by CST STUDIO SUITE at different frequencies, and demonstrate the intuitionistic power location at the metamaterial lens interfaces.

[Expression of thioredoxin-2 in human lens epithelial cells with oxidative damage and its significance].

Science.gov (United States)

Che, Xuanyi; Zhao, Qingxia; Li, Di

2018-03-28

To explore whether thioredoin-2 (Trx-2) is involved in the development of cataract and to study the effect of Trx-2 on hydrogen peroxide (H2O2)-induced injury in human lens epithelial cells.
 Methods: A total of 10 volunteers (removing the lens due totraumatism) and 30 patients received phacoemulsification (age more than 60 years) were selected. The expression of Trx-2 protein in lens epithelial cells from cataract patients and volunteers were detected by the immunohistochemical streptavidin-peroxidase (SP) method. SRA01/04 cells were cultured and were divided into six groups according to different treatment: a control group, H2O2-treated groups at 20, 50 or 
100 μmol/L, a negative control group (transfected with pCMV6 plasmid plus 100 μmol/L H2O2), and a Trx-2 overexpression group (transfected with pCMV6-Trx-2 plasmid plus 100 μmol/L H2O2). Methyl thiazolyltetrazolium (MTT) assay and flow cytometry was performed to measure the cell viability and apoptosis for SRA01/04 cells, respectively. The activities of superoxide dismutase (SOD) and catalase (CAT), the content of glutathione (GSH) and malondialdehyde (MDA) in human lens epithelial cells were measured via chemical chromatometry. Western blot was used to measure the protein levels of Trx-2, B-cell lymphoma 2 protein (Bcl-2), Bcl-2 associated X protein (Bax) and caspase-3.
 Results: Compared with the volunteers, the expression of Trx-2 was significantly decreased in lens epithelial cells in patients with cataract (PTrx-2 protein in the 20, 50 or 100 μmol/L H2O2 groups was decreased (all PTrx-2 and Bcl-2 expression and up-regulated Bax and caspase-3 expression (all PTrx-2 overexpression group (PTrx-2 and Bcl-2 expression and down-regulated Bax and caspase-3 expression (PTrx-2 might be involved in the apoptosis of lens epithelial cells in patients with cataract. The overexpression of Trx-2 obviously attenuated H2O2-induced injury of human lens epithelial cells, which might be associated with the

Aquaporin 0 plays a pivotal role in refractive index gradient development in mammalian eye lens to prevent spherical aberration

International Nuclear Information System (INIS)

Kumari, S. Sindhu; Varadaraj, Kulandaiappan

2014-01-01

Highlights: • Intact AQP0 functions as fiber cell-to-fiber cell adhesion protein. • AQP0 facilitates reduction in extracellular space and lens water content. • AQP0 adhesion function aids in lens refractive index gradient (RING) formation. • AQP0 prevents lens spherical aberration by establishing RING. • AQP0 is critical for lens transparency and homeostasis. - Abstract: Aquaporin 0 (AQP0) is a transmembrane channel that constitutes ∼45% of the total membrane protein of the fiber cells in mammalian lens. It is critical for lens transparency and homeostasis as mutations and knockout cause autosomal dominant lens cataract. AQP0 functions as a water channel and as a cell-to-cell adhesion (CTCA) molecule in the lens. Our recent in vitro studies showed that the CTCA function of AQP0 could be crucial to establish lens refractive index gradient (RING). However, there is a lack of in vivo data to corroborate the role of AQP0 as a fiber CTCA molecule which is critical for creating lens RING. The present investigation is undertaken to gather in vivo evidence for the involvement of AQP0 in developing lens RING. Lenses of wild type (WT) mouse, AQP0 knockout (heterozygous, AQP0 +/− ) and AQP0 knockout lens transgenically expressing AQP1 (heterozygous AQP0 +/− /AQP1 +/− ) mouse models were used for the study. Data on AQP0 protein profile of intact and N- and/or C-terminal cleaved AQP0 in the lens by MALDI-TOF mass spectrometry and SDS–PAGE revealed that outer cortex fiber cells have only intact AQP0 of ∼28 kDa, inner cortical and outer nuclear fiber cells have both intact and cleaved forms, and inner nuclear fiber cells have only cleaved forms (∼26–24 kDa). Knocking out of 50% of AQP0 protein caused light scattering, spherical aberration (SA) and cataract. Restoring the lost fiber cell membrane water permeability (P f ) by transgene AQP1 did not reinstate complete lens transparency and the mouse lenses showed light scattering and SA. Transmission and

Daylighting System Based on Novel Design of Linear Fresnel lens

Directory of Open Access Journals (Sweden)

Thanh Tuan Pham

2017-10-01

Full Text Available In this paper, we present a design and optical simulation of a daylighting system using a novel design of linear Fresnel lens, which is constructed based on the conservation of optical path length and edge ray theorem. The linear Fresnel lens can achieve a high uniformity by using a new idea of design in which each groove of the lens distributes sunlight uniformly over the receiver so that the whole lens also uniformly distributes sunlight over the receiver. In this daylighting system, the novel design of linear Fresnel lens significantly improves the uniformity of collector and distributor. Therefore, it can help to improve the performance of the daylighting system. The structure of the linear Fresnel lenses is designed by using Matlab. Then, the structure of lenses is appreciated by ray tracing in LightToolsTM to find out the optimum lens shape. In addition, the simulation is performed by using LightToolsTM to estimate the efficiency of the daylighting system. The results show that the designed collector can achieve the efficiency of ~80% with the tolerance of ~0.60 and the concentration ratio of 340 times, while the designed distributor can reach a high uniformity of >90%.

Metamaterial-based half Maxwell fish-eye lens for broadband directive emissions

Science.gov (United States)

Dhouibi, Abdallah; Nawaz Burokur, Shah; de Lustrac, André; Priou, Alain

2013-01-01

The broadband directive emission from a metamaterial surface is numerically and experimentally reported. The metasurface, composed of non-resonant complementary closed ring structures, is designed to obey the refractive index of a half Maxwell fish-eye lens. A planar microstrip Vivaldi antenna is used as transverse magnetic polarized wave launcher for the lens. A prototype of the lens associated with its feed structure has been fabricated using standard lithography techniques. To experimentally demonstrate the broadband focusing properties and directive emissions, both the far-field radiation patterns and the near-field distributions have been measured. Measurements agree quantitatively and qualitatively with theoretical simulations.

Electro-optically actuated liquid-lens zoom

Science.gov (United States)

Pütsch, O.; Loosen, P.

2012-06-01

Progressive miniaturization and mass market orientation denote a challenge to the design of dynamic optical systems such as zoom-lenses. Two working principles can be identified: mechanical actuation and application of active optical components. Mechanical actuation changes the focal length of a zoom-lens system by varying the axial positions of optical elements. These systems are limited in speed and often require complex coupled movements. However, well established optical design approaches can be applied. In contrast, active optical components change their optical properties by varying their physical structure by means of applying external electric signals. An example are liquidlenses which vary their curvatures to change the refractive power. Zoom-lenses benefit from active optical components in two ways: first, no moveable structures are required and second, fast response characteristics can be realized. The precommercial development of zoom-lenses demands simplified and cost-effective system designs. However the number of efficient optical designs for electro-optically actuated zoom-lenses is limited. In this paper, the systematic development of an electro-optically actuated zoom-lens will be discussed. The application of aberration polynomials enables a better comprehension of the primary monochromatic aberrations at the lens elements during a change in magnification. This enables an enhanced synthesis of the system behavior and leads to a simplified zoom-lens design with no moving elements. The change of focal length is achieved only by varying curvatures of targeted integrated electro-optically actuated lenses.

Changes in the internal structure of the human crystalline lens with diabetes mellitus type 1 and type 2

NARCIS (Netherlands)

Wiemer, N.G.M.; Dubbelman, M.; Hermans, E.A.; Ringens, P.J.; Polak, B.C.P.

2008-01-01

Purpose: To investigate the effect of diabetes mellitus (DM) type 1 and type 2 on the internal structure of the lens. Design: Observational cross-sectional study. Participants and Controls: One hundred seven patients with DM type 1, 106 patients with DM type 2, and 75 healthy control subjects.

An acoustic Maxwell’s fish-eye lens based on gradient-index metamaterials

International Nuclear Information System (INIS)

Yuan Bao-guo; Tian Ye; Cheng Ying; Liu Xiao-jun

2016-01-01

We have proposed a two-dimensional acoustic Maxwell’s fish-eye lens by using the gradient-index metamaterials with space-coiling units. By adjusting the structural parameters of the units, the refractive index can be gradually varied, which is key role to design the acoustic fish-eye lens. As predicted by ray trajectories on a virtual sphere, the proposed lens has the capability to focus the acoustic wave irradiated from a point source at the surface of the lens on the diametrically opposite side of the lens. The broadband and low loss performance is further demonstrated for the lens. The proposed acoustic fish-eye lens is expected to have the potential applications in directional acoustic coupler or coherent ultrasonic imaging. (paper)

SDSL-ESR-based protein structure characterization.

Science.gov (United States)

Strancar, Janez; Kavalenka, Aleh; Urbancic, Iztok; Ljubetic, Ajasja; Hemminga, Marcus A

2010-03-01

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.

Structure and non-structure of centrosomal proteins.

Science.gov (United States)

Dos Santos, Helena G; Abia, David; Janowski, Robert; Mortuza, Gulnahar; Bertero, Michela G; Boutin, Maïlys; Guarín, Nayibe; Méndez-Giraldez, Raúl; Nuñez, Alfonso; Pedrero, Juan G; Redondo, Pilar; Sanz, María; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, José M; Gonzalez, Cayetano; Reina, José; Valpuesta, José M; Vernos, Isabelle; Zabala, Juan C; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis

2013-01-01

Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

Post-lens tear turbidity and visual quality after scleral lens wear.

Science.gov (United States)

Carracedo, Gonzalo; Serramito-Blanco, Maria; Martin-Gil, Alba; Wang, Zicheng; Rodriguez-Pomar, Candela; Pintor, Jesús

2017-11-01

The aim was to evaluate the turbidity and thickness of the post-lens tear layer and its effect on visual quality in patients with keratoconus after the beginning of lens wear and before lens removal at the end of eight hours. Twenty-six patients with keratoconus (aged 36.95 ± 8.95 years) participated voluntarily in the study. The sample was divided into two groups: patients with intrastromal corneal ring (ICRS group) and patients without ICRS (KC group). Distance visual acuity (VA), contrast sensitivity, pachymetry, post-lens tear layer height and post-lens tear layer turbidity (percentage area occupied and number of particles per mm 2 ) were evaluated with optical coherence tomography before and after wearing a scleral lens. A significant increase of turbidity was found in all groups assessed (p turbidity parameters with distance VA but no correlation between turbidity and post-lens tear layer thickness at the beginning was found (p > 0.05). A strong correlation in all groups between the post-lens tear layer at the beginning and differences of tear layer thickness between two measures was also found (p turbidity. © 2017 Optometry Australia.

Disinfection capacity of PuriLens contact lens cleaning unit against Acanthamoeba.

Science.gov (United States)

Hwang, Thomas S; Hyon, Joon Young; Song, Jae Kyung; Reviglio, Victor E; Spahr, Harry T; O'Brien, Terrence P

2004-01-01

The PuriLens contact lens system is indicated for cleaning and disinfection of soft (hydrophilic) contact lenses by means of subsonic agitation to remove lens deposits and microorganisms, and ultraviolet irradiation of the storage solution for disinfection. The capacity of the PuriLens system to disinfect storage solutions contaminated with known concentrations of Staphylococcus aureus, Pseudomonas aeruginosa, and Acanthamoeba species was evaluated. An in vitro assessment of the antibacterial and antiparasitic efficacy of the PuriLens system was performed. Separated batches of the storage solution for the cleansing system were contaminated with stock strains of S. aureus and P. aeruginosa. A comparison of the microbiologic content was made between the solution before and after the cycle. The PuriLens system effectively eradicated S. aureus and P. aeruginosa organisms after a 15-minute cycle. However, viable cysts of acanthamoeba were recovered in the solution after the 15-minute cycle. The PuriLens system is highly efficient in protecting against contamination with common bacterial ocular pathogens. Acanthamoeba cysts, however, can survive in the solution or contact lens bath undergoing integrated subsonic debridement and indirect ultraviolet light disinfection. Use of chemical disinfecting solutions that contain agents such as chlorhexidine or other cationic antiseptics may be advisable in conjunction with use of the PuriLens device, especially in high-risk settings.

The Effect of the Crystalline Lens on Central Vault After Implantable Collamer Lens Implantation.

Science.gov (United States)

Qi, Meng-Ying; Chen, Qian; Zeng, Qing-Yan

2017-08-01

To identify associations between crystalline lens-related factors and central vault after Implantable Collamer Lens (ICL) (Staar Surgical, Monrovia, CA) implantation. This retrospective clinical study included 320 eyes from 186 patients who underwent ICL implantation surgery. At 1 year after surgery, the central vault was measured using anterior segment optical coherence tomography. Preoperative anterior chamber depth, lens thickness, lens position (lens position = anterior chamber depth + 1/2 lens thickness), and vault were analyzed to investigate the effects of lens-related factors on postoperative vault. The mean vault was 513 ± 215 µm at 1 year after surgery. Vault was positively correlated with preoperative anterior chamber depth (r = 0.495, P lens position (r = 0.371, P lens thickness (r = -0.262, P lens position than eyes in the other two vault groups (which had vaults ≥ 250 µm) (P lens position less than 5.1 mm had greatly reduced vaults (P lens could have an important influence on postoperative vault. Eyes with a shallower anterior chamber and a forward lens position will have lower vaults. [J Refract Surg. 2017;33(8):519-523.]. Copyright 2017, SLACK Incorporated.

A lazy way to design infrared lens

Science.gov (United States)

Qiu, RongSheng; Wu, JianDong; Chen, LongJiang; Yu, Kun; Pang, HaoJun; Hu, BaiZhen

2017-08-01

We designed a compact middle-wave infrared (MWIR) lens with a large focal length ratio (about 1.5:1), used in the 3.7 to 4.8 μm range. The lens is consisted of a compact front group and a re-imaging group. Thanks to the compact front group configuration, it is possible to install a filter wheel mechanism in such a tight space. The total track length of the lens is about 50mm, which includes a 2mm thick protective window and a cold shield of 12mm. The full field of view of the lens is about 3.6°, and F number is less than 1.6, the image circle is about 4.6mm in diameter. The design performance of the lens reaches diffraction limitation, and doesn't change a lot during a temperature range of -40°C +60°C. This essay proposed a stepwise design method of infrared optical system guided by the qualitative approach. The method fully utilize the powerful global optimization ability, with a little effort to write code snippet in optical design software, frees optical engineer from tedious calculation of the original structure.

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

Expression of truncated PITX3 in the developing lens leads to microphthalmia and aphakia in mice.

Directory of Open Access Journals (Sweden)

Kenta Wada

Full Text Available Microphthalmia is a severe ocular disorder, and this condition is typically caused by mutations in transcription factors that are involved in eye development. Mice carrying mutations in these transcription factors would be useful tools for defining the mechanisms underlying developmental eye disorders. We discovered a new spontaneous recessive microphthalmos mouse mutant in the Japanese wild-derived inbred strain KOR1/Stm. The homozygous mutant mice were histologically characterized as microphthalmic by the absence of crystallin in the lens, a condition referred to as aphakia. By positional cloning, we identified the nonsense mutation c.444C>A outside the genomic region that encodes the homeodomain of the paired-like homeodomain transcription factor 3 gene (Pitx3 as the mutation responsible for the microphthalmia and aphakia. We examined Pitx3 mRNA expression of mutant mice during embryonic stages using RT-PCR and found that the expression levels are higher than in wild-type mice. Pitx3 over-expression in the lens during developmental stages was also confirmed at the protein level in the microphthalmos mutants via immunohistochemical analyses. Although lens fiber differentiation was not observed in the mutants, strong PITX3 protein signals were observed in the lens vesicles of the mutant lens. Thus, we speculated that abnormal PITX3, which lacks the C-terminus (including the OAR domain as a result of the nonsense mutation, is expressed in mutant lenses. We showed that the expression of the downstream genes Foxe3, Prox1, and Mip was altered because of the Pitx3 mutation, with large reductions in the lens vesicles in the mutants. Similar profiles were observed by immunohistochemical analysis of these proteins. The expression profiles of crystallins were also altered in the mutants. Therefore, we speculated that the microphthalmos/aphakia in this mutant is caused by the expression of truncated PITX3, resulting in the abnormal expression of

Aquaporin 0 plays a pivotal role in refractive index gradient development in mammalian eye lens to prevent spherical aberration

Energy Technology Data Exchange (ETDEWEB)

Kumari, S. Sindhu [Physiology and Biophysics, Stony Brook University, Stony Brook, NY (United States); Varadaraj, Kulandaiappan, E-mail: kulandaiappan.varadaraj@stonybrook.edu [Physiology and Biophysics, Stony Brook University, Stony Brook, NY (United States); SUNY Eye Institute, New York, NY (United States)

2014-10-03

Highlights: • Intact AQP0 functions as fiber cell-to-fiber cell adhesion protein. • AQP0 facilitates reduction in extracellular space and lens water content. • AQP0 adhesion function aids in lens refractive index gradient (RING) formation. • AQP0 prevents lens spherical aberration by establishing RING. • AQP0 is critical for lens transparency and homeostasis. - Abstract: Aquaporin 0 (AQP0) is a transmembrane channel that constitutes ∼45% of the total membrane protein of the fiber cells in mammalian lens. It is critical for lens transparency and homeostasis as mutations and knockout cause autosomal dominant lens cataract. AQP0 functions as a water channel and as a cell-to-cell adhesion (CTCA) molecule in the lens. Our recent in vitro studies showed that the CTCA function of AQP0 could be crucial to establish lens refractive index gradient (RING). However, there is a lack of in vivo data to corroborate the role of AQP0 as a fiber CTCA molecule which is critical for creating lens RING. The present investigation is undertaken to gather in vivo evidence for the involvement of AQP0 in developing lens RING. Lenses of wild type (WT) mouse, AQP0 knockout (heterozygous, AQP0{sup +/−}) and AQP0 knockout lens transgenically expressing AQP1 (heterozygous AQP0{sup +/−}/AQP1{sup +/−}) mouse models were used for the study. Data on AQP0 protein profile of intact and N- and/or C-terminal cleaved AQP0 in the lens by MALDI-TOF mass spectrometry and SDS–PAGE revealed that outer cortex fiber cells have only intact AQP0 of ∼28 kDa, inner cortical and outer nuclear fiber cells have both intact and cleaved forms, and inner nuclear fiber cells have only cleaved forms (∼26–24 kDa). Knocking out of 50% of AQP0 protein caused light scattering, spherical aberration (SA) and cataract. Restoring the lost fiber cell membrane water permeability (P{sub f}) by transgene AQP1 did not reinstate complete lens transparency and the mouse lenses showed light scattering and SA

Measurement of Crystalline Lens Volume During Accommodation in a Lens Stretcher.

Science.gov (United States)

Marussich, Lauren; Manns, Fabrice; Nankivil, Derek; Maceo Heilman, Bianca; Yao, Yue; Arrieta-Quintero, Esdras; Ho, Arthur; Augusteyn, Robert; Parel, Jean-Marie

2015-07-01

To determine if the lens volume changes during accommodation. The study used data acquired on 36 cynomolgus monkey lenses that were stretched in a stepwise fashion to simulate disaccommodation. At each step, stretching force and dioptric power were measured and a cross-sectional image of the lens was acquired using an optical coherence tomography system. Images were corrected for refractive distortions and lens volume was calculated assuming rotational symmetry. The average change in lens volume was calculated and the relation between volume change and power change, and between volume change and stretching force, were quantified. Linear regressions of volume-power and volume-force plots were calculated. The mean (± SD) volume in the unstretched (accommodated) state was 97 ± 8 mm3. On average, there was a small but statistically significant (P = 0.002) increase in measured lens volume with stretching. The mean change in lens volume was +0.8 ± 1.3 mm3. The mean volume-power and volume-load slopes were -0.018 ± 0.058 mm3/D and +0.16 ± 0.40 mm3/g. Lens volume remains effectively constant during accommodation, with changes that are less than 1% on average. This result supports a hypothesis that the change in lens shape with accommodation is accompanied by a redistribution of tissue within the capsular bag without significant compression of the lens contents or fluid exchange through the capsule.

Properties of Fiber Cell Plasma Membranes Isolated from the Cortex and Nucleus of the Porcine Eye Lens

Science.gov (United States)

Mainali, Laxman; Raguz, Marija; O’Brien, William J.; Subczynski, Witold K.

2012-01-01

The organization and physical properties of the lipid bilayer portion of intact cortical and nuclear fiber cell plasma membranes isolated from the eyes lenses of two-year-old pigs were studied using electron paramagnetic resonance (EPR) spin-labeling. Membrane fluidity, hydrophobicity, and the oxygen transport parameter (OTP) were assessed from the EPR spectra of precisely positioned spin labels. Intact cortical and nuclear membranes, which include membrane proteins, were found to contain three distinct lipid environments. These lipid environments were termed the bulk lipid domain, boundary lipid domain, and trapped lipid domain (lipids in protein aggregates). The amount of boundary and trapped lipids was greater in intact nuclear membranes than in cortical membranes. The properties of intact membranes were compared with the organization and properties of lens lipid membranes made of the total lipid extracts from the lens cortex or nucleus. In cortical lens lipid membranes, only one homogenous environment was detected, which was designated as a bulk lipid domain (phospholipid bilayer saturated with cholesterol). Lens lipid membranes prepared from the lens nucleus possessed two domains, assigned as a bulk lipid domain and a cholesterol bilayer domain (CBD). In intact nuclear membranes, it was difficult to discriminate the CBD, which was clearly detected in nuclear lens lipid membranes because the OTP measured in the CBD is the same as in the domain formed by trapped lipids. The two domains unique to intact membranes—namely, the domain formed by boundary lipids and the domain formed by trapped lipids—were most likely formed due to the presence of membrane proteins. It is concluded that formation of rigid and practically impermeable domains is enhanced in the lens nucleus, indicating changes in membrane composition that may help to maintain low oxygen concentration in this lens region. PMID:22326289

The role of macromolecular crowding in the evolution of lens crystallins with high molecular refractive index

International Nuclear Information System (INIS)

Zhao, Huaying; Magone, M Teresa; Schuck, Peter

2011-01-01

Crystallins are present in the lens at extremely high concentrations in order to provide transparency and generate a high refractive power of the lens. The crystallin families prevalent in the highest density lens tissues are γ-crystallins in vertebrates and S-crystallins in cephalopods. As shown elsewhere, in parallel evolution, both have evolved molecular refractive index increments 5–10% above those of most proteins. Although this is a small increase, it is statistically very significant and can be achieved only by very unusual amino acid compositions. In contrast, such a molecular adaptation to aid in the refractive function of the lens did not occur in crystallins that are preferentially located in lower density lens tissues, such as vertebrate α-crystallin and taxon-specific crystallins. In the current work, we apply a model of non-interacting hard spheres to examine the thermodynamic contributions of volume exclusion at lenticular protein concentrations. We show that the small concentration decrease afforded by the higher molecular refractive index increment of crystallins can amplify nonlinearly to produce order of magnitude differences in chemical activities, and lead to reduced osmotic pressure and the reduced propensity for protein aggregation. Quantitatively, this amplification sets in only at protein concentrations as high as those found in hard lenses or the nucleus of soft lenses, in good correspondence to the observed crystallin properties in different tissues and different species. This suggests that volume exclusion effects provide the evolutionary driving force for the unusual refractive properties and the unusual amino acid compositions of γ-crystallins and S-crystallins

Diffraction enhanced X-ray imaging of mammals crystalline lens

International Nuclear Information System (INIS)

Antunes, A.; Hoennicke, M.G.; Safatle, A.M.V.; Cusatis, C.; Moraes Barros, P.S.; Morelhao, S.L.

2005-01-01

Crystalline lenses are transparent biological materials where the organization of the lens fibers can also be affected by changes at molecular level, and therefore the structure and morphology of the tissue can be correlated to the loss of transparency of the lens. In this work, internal structure of mammal lenses regarding the long-range ordering of the fibers are investigated by diffraction enhanced X-ray imaging (DEI) radiography. Moreover, DEI and absorption X-ray synchrotron radiographs for healthy and cataractous crystalline lenses are compared. Significant differences in healthy and cataractous crystalline lenses are observed

NAPS: Network Analysis of Protein Structures

Science.gov (United States)

Chakrabarty, Broto; Parekh, Nita

2016-01-01

Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

Physical changes in bovine lens homogenate following ultraviolet irradiation and their prevention by some compounds

International Nuclear Information System (INIS)

Ohmori, Shinji; Nose, Hideko

1985-01-01

Exposure of the dialyzed supernatant of bovine lens homogenate to ultraviolet (UV) light led to increases in its turbidity, pigmentation, and viscosity. These photochemically induced alterations of lens proteins were prevented by glutathione, cysteine and N-acetylcysteine, but not by ascorbic acid, S-(1,2-dicarboxyethyl)-glutathione or dulcitol. (author)

Hard sphere-like glass transition in eye lens α-crystallin solutions.

Science.gov (United States)

Foffi, Giuseppe; Savin, Gabriela; Bucciarelli, Saskia; Dorsaz, Nicolas; Thurston, George M; Stradner, Anna; Schurtenberger, Peter

2014-11-25

We study the equilibrium liquid structure and dynamics of dilute and concentrated bovine eye lens α-crystallin solutions, using small-angle X-ray scattering, static and dynamic light scattering, viscometry, molecular dynamics simulations, and mode-coupling theory. We find that a polydisperse Percus-Yevick hard-sphere liquid-structure model accurately reproduces both static light scattering data and small-angle X-ray scattering liquid structure data from α-crystallin solutions over an extended range of protein concentrations up to 290 mg/mL or 49% vol fraction and up to ca. 330 mg/mL for static light scattering. The measured dynamic light scattering and viscosity properties are also consistent with those of hard-sphere colloids and show power laws characteristic of an approach toward a glass transition at α-crystallin volume fractions near 58%. Dynamic light scattering at a volume fraction beyond the glass transition indicates formation of an arrested state. We further perform event-driven molecular dynamics simulations of polydisperse hard-sphere systems and use mode-coupling theory to compare the measured dynamic power laws with those of hard-sphere models. The static and dynamic data, simulations, and analysis show that aqueous eye lens α-crystallin solutions exhibit a glass transition at high concentrations that is similar to those found in hard-sphere colloidal systems. The α-crystallin glass transition could have implications for the molecular basis of presbyopia and the kinetics of molecular change during cataractogenesis.

Design and analysis of all-dielectric subwavelength focusing flat lens

Science.gov (United States)

Turduev, M.; Bor, E.; Kurt, H.

2017-09-01

In this letter, we numerically designed and experimentally demonstrated a compact photonic structure for the subwavelength focusing of light using all-dielectric absorption-free and nonmagnetic scattering objects distributed in an air medium. In order to design the subwavelength focusing flat lens, an evolutionary algorithm is combined with the finite-difference time-domain method for determining the locations of cylindrical scatterers. During the multi-objective optimization process, a specific objective function is defined to reduce the full width at half maximum (FWHM) and diminish side lobe level (SLL) values of light at the focal point. The time-domain response of the optimized flat lens exhibits subwavelength light focusing with an FWHM value of 0.19λ and an SLL value of 0.23, where λ denotes the operating wavelength of light. Experimental analysis of the proposed flat lens is conducted in a microwave regime and findings exactly verify the numerical results with an FWHM of 0.192λ and an SLL value of 0.311 at the operating frequency of 5.42 GHz. Moreover, the designed flat lens provides a broadband subwavelength focusing effect with a 9% bandwidth covering frequency range of 5.10 GHz-5.58 GHz, where corresponding FWHM values remain under 0.21λ. Also, it is important to note that the designed flat lens structure performs a line focusing effect. Possible applications of the designed structure in telecom wavelengths are speculated upon for future perspectives. Namely, the designed structure can perform well in photonic integrated circuits for different fields of applications such as high efficiency light coupling, imaging and optical microscopy, with its compact size and ability for strong focusing.

AutoLens: Automated Modeling of a Strong Lens's Light, Mass and Source

Science.gov (United States)

Nightingale, J. W.; Dye, S.; Massey, Richard J.

2018-05-01

This work presents AutoLens, the first entirely automated modeling suite for the analysis of galaxy-scale strong gravitational lenses. AutoLens simultaneously models the lens galaxy's light and mass whilst reconstructing the extended source galaxy on an adaptive pixel-grid. The method's approach to source-plane discretization is amorphous, adapting its clustering and regularization to the intrinsic properties of the lensed source. The lens's light is fitted using a superposition of Sersic functions, allowing AutoLens to cleanly deblend its light from the source. Single component mass models representing the lens's total mass density profile are demonstrated, which in conjunction with light modeling can detect central images using a centrally cored profile. Decomposed mass modeling is also shown, which can fully decouple a lens's light and dark matter and determine whether the two component are geometrically aligned. The complexity of the light and mass models are automatically chosen via Bayesian model comparison. These steps form AutoLens's automated analysis pipeline, such that all results in this work are generated without any user-intervention. This is rigorously tested on a large suite of simulated images, assessing its performance on a broad range of lens profiles, source morphologies and lensing geometries. The method's performance is excellent, with accurate light, mass and source profiles inferred for data sets representative of both existing Hubble imaging and future Euclid wide-field observations.

Interim report of the JHPS expert committee on radiation protection of the lens of the eye (1). Overview of the lens, radiogenic cataract, and equivalent dose limit for the lens newly recommended by the ICRP

International Nuclear Information System (INIS)

Akahane, Keiichi; Tatsuzaki, Hideo; Iimoto, Takeshi; Ichiji, Takeshi; Hamada, Nobuyuki; Fujimichi, Yuki; Iwai, Satoshi; Ohguchi, Hiroyuki; Ohno, Kazuko; Yamauchi, Chiyo; Tsujimura, Norio; Hotta, Yutaka; Yamasaki, Tadashi; Yokoyama, Sumi

2014-01-01

In April 2011, the International Commission on Radiological Protection (ICRP) issued the statement on tissue reactions. This stimulated interest in many countries. The Expert Committee on Radiation Protection of the Lens of the Eye was established in the Japanese Health Physics Society, and in April 2013, started discussion about the international developments and recent studies related to the dosimetry of the lens of the eye. This committee now publishes the interim report consisting of parts I-VI. Of these, this Part I overviews the structure of the eye and lens, cataract types and the scientific evidence of its new dose threshold and equivalent dose limit newly recommended by the ICRP. (author)

Spatial pattern of cell geometry and cell-division orientation in zebrafish lens epithelium

Directory of Open Access Journals (Sweden)

Toshiaki Mochizuki

2014-09-01

Full Text Available Cell proliferation is a key regulator of tissue morphogenesis. We examined cell proliferation and cell division in zebrafish lens epithelium by visualizing cell-cycle phases and nuclear positions, using fluorescent-labeled geminin and histone proteins. Proliferation was low in the anterior region of lens epithelium and higher in the marginal zone anterior to the equator, suggesting that the proliferation zone, called the germinative zone, is formed in zebrafish lens. Interestingly, cell-division orientation was biased longitudinally in the anterior region, shifted from longitudinal to circumferential along the anterior–posterior axis of lens sphere, and was biased circumferentially in the peripheral region. These data suggest that cell-division orientation is spatially regulated in zebrafish lens epithelium. The Hertwig rule indicates that cells tend to divide along their long axes. Orientation of long axes and cell division were biased similarly in zebrafish lens epithelium, suggesting that cell geometry correlates with cell-division orientation. A cell adhesion molecule, E-cadherin, is expressed in lens epithelium. In a zebrafish e-cadherin mutant, the long axes and cell-division orientation were shifted more longitudinally. These data suggest that E-cadherin is required for the spatial pattern of cell geometry and cell-division orientation in zebrafish lens epithelium.

Optical integration of Pancharatnam-Berry phase lens and dynamical phase lens

International Nuclear Information System (INIS)

Ke, Yougang; Liu, Yachao; Zhou, Junxiao; Liu, Yuanyuan; Luo, Hailu; Wen, Shuangchun

2016-01-01

In the optical system, most elements such as lens, prism, and optical fiber are made of silica glass. Therefore, integrating Pancharatnam-Berry phase elements into silica glass has potential applications in the optical system. In this paper, we take a lens, for example, which integrates a Pancharatnam-Berry phase lens into a conventional plano-convex lens. The spin states and positions of focal points can be modulated by controlling the polarization states of the incident beam. The proposed lens has a high transmission efficiency, and thereby acts as a simple and powerful tool to manipulate spin photons. Furthermore, the method can be conveniently extended to the optical fiber and laser cavity, and may provide a route to the design of the spin-photonic devices.

Converging or Diverging Lens?

Science.gov (United States)

Branca, Mario

2013-01-01

Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

Fast loop modeling for protein structures

Science.gov (United States)

Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

2015-03-01

X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

Placement of a crystalline lens and intraocular lens: Retinal image quality.

Science.gov (United States)

Siedlecki, Damian; Nowak, Jerzy; Zajac, Marek

2006-01-01

The influence of changes of both crystalline lens and intraocular lens (IOL) misalignment on the retinal image quality was investigated. The optical model of the eye used in investigations was the Liou-Brennan model, which is commonly considered as one of the most anatomically accurate. The original crystalline lens from this model was replaced with an IOL, made of rigid polymethylmethacrylate, in a way that recommend obligatory procedures. The modifications that were made both for crystalline lens and IOL were the longitudinal, the transversal, and the angular displacement.

Characterization of the Effects of Hyperbaric Oxygen on the Biochemical and Optical Properties of the Bovine Lens.

Science.gov (United States)

Lim, Julie C; Vaghefi, Ehsan; Li, Bo; Nye-Wood, Mitchell G; Donaldson, Paul J

2016-04-01

To assess the morphologic, biochemical, and optical properties of bovine lenses treated with hyperbaric oxygen. Lenses were exposed to hyperbaric nitrogen (HBN) or hyperbaric oxygen (HBO) for 5 or 15 hours, lens transparency was assessed using bright field microscopy and lens morphology was visualized using confocal microscopy. Lenses were dissected into the outer cortex, inner cortex, and core, and glutathione (GSH) and malondialdehyde (MDA) measured. Gel electrophoresis and Western blotting were used to detect high molecular weight aggregates (HMW) and glutathione mixed protein disulfides (PSSG). T2-weighted MRI was used to measure lens geometry and map the water/protein ratio to allow gradient refractive index (GRIN) profiles to be calculated. Optical modeling software calculated the change in lens optical power, and an anatomically correct model of the light pathway of the bovine eye was used to determine the effects of HBN and HBO on focal length and overall image quality. Lenses were transparent and lens morphology similar between HBN- and HBO-treated lenses. At 5- and 15-hour HBO exposure, GSH and GSSG were depleted and MDA increased in the core. Glutathione mixed protein disulfides were detected in the outer and inner cortex only with no appearance of HMW. Optical changes were detectable only with 15-hour HBO treatment with a decrease in the refractive index of the core, slightly reduced lens thickness, and an increase in optimal focal length, consistent with a hyperopic shift. This system may serve as a model to study changes that occur with advanced aging rather than nuclear cataract formation per se.

Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

International Nuclear Information System (INIS)

Tuncbag, Nurcan; Gursoy, Attila; Keskin, Ozlem

2011-01-01

The vast majority of the chores in the living cell involve protein–protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein–protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations

Refractive neutron lens

International Nuclear Information System (INIS)

Petrov, P.V.; Kolchevsky, N.N.

2013-01-01

Model of the refractive neutron lens is proposed. System of N lenses acts as one thin lens with a complex refraction index n*. The maximum number N max of individual lenses for 'thick' neutron lens is calculated. Refractive neutron lens properties (resolution, focal depth) as function of resolution factor F 0 =ρbc/μ and depth of field factor dF 0 =λF 0 =λρbc/μ are calculated. It is shown that micro resolution of the refractive neutron optics is far from the wavelength in size and its open possibilities for progress in refractive neutron optics. (authors)

Structural anatomy of telomere OB proteins.

Science.gov (United States)

Horvath, Martin P

2011-10-01

Telomere DNA-binding proteins protect the ends of chromosomes in eukaryotes. A subset of these proteins are constructed with one or more OB folds and bind with G+T-rich single-stranded DNA found at the extreme termini. The resulting DNA-OB protein complex interacts with other telomere components to coordinate critical telomere functions of DNA protection and DNA synthesis. While the first crystal and NMR structures readily explained protection of telomere ends, the picture of how single-stranded DNA becomes available to serve as primer and template for synthesis of new telomere DNA is only recently coming into focus. New structures of telomere OB fold proteins alongside insights from genetic and biochemical experiments have made significant contributions towards understanding how protein-binding OB proteins collaborate with DNA-binding OB proteins to recruit telomerase and DNA polymerase for telomere homeostasis. This review surveys telomere OB protein structures alongside highly comparable structures derived from replication protein A (RPA) components, with the goal of providing a molecular context for understanding telomere OB protein evolution and mechanism of action in protection and synthesis of telomere DNA.

Protein Structure and the Sequential Structure of mRNA

DEFF Research Database (Denmark)

Brunak, Søren; Engelbrecht, Jacob

1996-01-01

entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment, By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets, These signals do not originate from......A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed, We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting...... protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain, A complete search for GenBank nucleotide sequences coding for structural...

Micron-scale lens array having diffracting structures

Science.gov (United States)

Goldberg, Kenneth A

2013-10-29

A novel micron-scale lens, a microlens, is engineered to concentrate light efficiently onto an area of interest, such as a small, light-sensitive detector element in an integrated electronic device. Existing microlens designs imitate the form of large-scale lenses and are less effective at small sizes. The microlenses described herein have been designed to accommodate diffraction effects, which dominate the behavior of light at small length scales. Thus a new class of light-concentrating optical elements with much higher relative performance has been created. Furthermore, the new designs are much easier to fabricate than previous designs.

Exchange of tears under a contact lens is driven by distortions of the contact lens.

Science.gov (United States)

Maki, Kara L; Ross, David S

2014-12-01

We studied the flow of the post-lens tear film under a soft contact lens to understand how the design parameters of contact lenses can affect ocular health. When a soft contact lens is inserted, the blinking eyelid causes the lens to stretch in order to conform to the shape of the eye. The deformed contact lens acts to assume its un-deformed shape and thus generates a suction pressure in the post-lens tear film. In consequence, the post-lens tear fluid moves; it responds to the suction pressure. The suction pressure may draw in fresh fluid from the edge of the lens, or it may eject fluid there, as the lens reassumes its un-deformed shape. In this article, we develop a mathematical model of the flow of the post-lens tear fluid in response to the mechanical suction pressure of a deformed contact lens. We predict the amount of exchange of fluid exchange under a contact lens and we explore the influence of the eye's shape on the rate of exchange of fluid. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

Science.gov (United States)

Bordoli, Lorenza; Schwede, Torsten

2012-01-01

Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

OpenAIRE

Bordoli, Lorenza; Schwede, Torsten

2012-01-01

Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of appl...

Peripheral Defocus of the Monkey Crystalline Lens With Accommodation in a Lens Stretcher

Science.gov (United States)

Maceo Heilman, Bianca; Manns, Fabrice; Ruggeri, Marco; Ho, Arthur; Gonzalez, Alex; Rowaan, Cor; Bernal, Andres; Arrieta, Esdras; Parel, Jean-Marie

2018-01-01

Purpose To characterize the peripheral defocus of the monkey crystalline lens and its changes with accommodation. Methods Experiments were performed on 15 lenses from 11 cynomolgus monkey eyes (age: 3.8–12.4 years, postmortem time: 33.5 ± 15.3 hours). The tissue was mounted in a motorized lens stretcher to allow for measurements of the lens in the accommodated (unstretched) and unaccommodated (stretched) states. A custom-built combined laser ray tracing and optical coherence tomography system was used to measure the paraxial on-axis and off-axis lens power for delivery angles ranging from −20° to +20° (in air). For each delivery angle, peripheral defocus was quantified as the difference between paraxial off-axis and on-axis power. The peripheral defocus of the lens was compared in the unstretched and stretched states. Results On average, the paraxial on-axis lens power was 52.0 ± 3.4 D in the unstretched state and 32.5 ± 5.1 D in the stretched state. In both states, the lens power increased with increasing delivery angle. From 0° to +20°, the relative peripheral lens power increased by 10.7 ± 1.4 D in the unstretched state and 7.5 ± 1.6 D in the stretched state. The change in field curvature with accommodation was statistically significant (P lens has greater curvature or relative peripheral power. Conclusions The cynomolgus monkey lens has significant accommodation-dependent curvature of field, which suggests that the lens asserts a significant contribution to the peripheral optical performance of the eye that also varies with the state of accommodation.

Electrophoretic study on intraspecific variations and interspecific relationships of marine catfishes (Siluriformes, Ariidae of Cananéia (São Paulo, Brazil: 1. General proteins of eye-lens and skeletic muscle

Directory of Open Access Journals (Sweden)

Hana Suzuki

1990-06-01

Full Text Available Cellulose acetate electrophoresis of eye-lens proteins and Polyacrylamide flat gel electrophoresis of skeletic muscle proteins of six species of marine catfishes were carried out. Genetic polymorphism only occured at one locus of the electropherograms of eye-lens of Cathorops spixii. Ontogenetic variations in the relative concentration of bands were found in the electropherograms of eye-lens and skeletic muscle proteins. The six species of catfishes can be identified by means of quantitative and qualitative differences in the electropherograms. Coefficients of similarity were determined by the band-counting method and UPGMA dendrograms were constructed to illustrate the interspecific relationships among the species.Eletroforeses de proteínas gerais de cristalinos e de músculo esquelético de seis espécies de bagres marinhos foram realizadas, respectivamente, em membranas de acetato de celulose e em géis de poliacrilamida. Polimorfismo genético ocorreu apenas em um locus de eletroferogramas do cristalino de Cathorops spixii. Variações ontogenéticas nas concentrações relativas das bandas foram observadas nos eletroferogramas do cristalino e do músculo esquelético. As seis espécies de bagres marinhos podem ser identificadas através das diferenças quantitativas e qualitativas nos eletroferogramas. Coeficientes de similaridade foram determinadas pelo método de contagem de bandas e dendrogramas UPGMA foram construídos para ilustrar as relações interespecíficas entre as espécies.

Compliance among soft contact lens wearers.

Science.gov (United States)

Kuzman, Tomislav; Kutija, Marija Barisić; Masnec, Sanja; Jandroković, Sonja; Mrazovac, Danijela; Jurisić, Darija; Skegro, Ivan; Kalauz, Miro; Kordić, Rajko

2014-12-01

Contact lens compliance is proven to be crucial for preventing lens wear-related complications because of the interdependence of the steps in lens care regime and their influence on lens system microbial contamination. Awareness of the patients' lens handling compliance as well as correct recognition of non-compliant behaviours is the basis for creating more targeted strategies for patient education. The aim of this study was to investigate compliance among soft contact lens (SCL) wearers in different aspects of lens care handling and wearing habits. In our research 50 asymptomatic lens wearers filled out a questionnaire containing demographic data, lens type, hygiene and wearing habits, lenses and lens care system replacement schedule and self-evaluation of contact lens handling hygiene. We established criteria of compliance according to available manufacturer's recommendations, prior literature and our clinical experience. Only 2 (4%) of patients were fully compliant SCL wearers. The most common non-compliant behaviours were insufficient lens solution soaking time (62%), followed by failure to daily exchange lens case solution and showering while wearing lenses. 44% of patients reported storing lenses in saline solution. Mean lens storage case replacement was 3.6 months, with up to 78% patients replacing lens case at least once in 3 months. Average grade in self evaluating level of compliance was very good (4 +/- 0.78) (from 1-poor level of hygiene to 5-great level of hygiene). Lens wearers who reported excessive daily lens wear and more than 10 years of lens wearing experience were also found to be less compliant with other lens system care procedures. (t = -2.99, df=47, p rate, self grading was relatively high. Therefore, these results indicate the need for patient education and encouragement of better lens wearing habits and all of the lens maintenance steps at each patient visit.

Comparison of clear lens extraction and collamer lens implantation in high myopia

Directory of Open Access Journals (Sweden)

Ahmed M Emarah

2010-05-01

Full Text Available Ahmed M Emarah, Mostafa A El-Helw, Hazem M YassinCairo University, Cairo, EgyptAim: To compare the outcomes of clear lens extraction and collamer lens implantation in high myopia.Patients and methods: Myopic patients younger than 40 years old with more than 12 diopters of myopia or who were not fit for laser-assisted in situ keratomileusis were included. Group 1 comprised patients undergoing clear lens extraction and Group 2 patients received the Visian implantable collamer lens. Outcome and complications were evaluated.Results: Postoperative best corrected visual acuity was -0.61 ± 0.18 in Group 1 and 0.79 ± 0.16 in Group 2. In Group 1, 71.4% achieved a postoperative uncorrected visual acuity better than the preoperative best corrected visual acuity, while only 51.8% patients achieved this in Group 2. Intraocular pressure decreased by 12.55% in Group 1, and increased by 15.11% in Group 2. Corneal endothelial cell density decreased by 4.47% in Group 1 and decreased by 5.67% in Group 2. Posterior capsule opacification occurred in Group 1. In Group 2, lens opacification occurred in 11.11%, significant pigment dispersion in 3.7%, and pupillary block glaucoma in 3.7%.Conclusion: Clear lens extraction presents less of a financial load up front, and less likelihood of the need for a secondary intervention in the future. Clear lens extraction is a more viable solution in developing countries with limited financial resources.Keywords: clear lens extraction, implantable collamer lens, myopia

Beta-structures in fibrous proteins.

Science.gov (United States)

Kajava, Andrey V; Squire, John M; Parry, David A D

2006-01-01

The beta-form of protein folding, one of the earliest protein structures to be defined, was originally observed in studies of silks. It was then seen in early studies of synthetic polypeptides and, of course, is now known to be present in a variety of guises as an essential component of globular protein structures. However, in the last decade or so it has become clear that the beta-conformation of chains is present not only in many of the amyloid structures associated with, for example, Alzheimer's Disease, but also in the prion structures associated with the spongiform encephalopathies. Furthermore, X-ray crystallography studies have revealed the high incidence of the beta-fibrous proteins among virulence factors of pathogenic bacteria and viruses. Here we describe the basic forms of the beta-fold, summarize the many different new forms of beta-structural fibrous arrangements that have been discovered, and review advances in structural studies of amyloid and prion fibrils. These and other issues are described in detail in later chapters.

Millimeter positron focusing using a hybrid lens design

International Nuclear Information System (INIS)

Cheung, C.K.; Kwan, P.Y.; Shan, Y.Y.; Naik, P.S.; Weng, H.M.; Beling, C.D.; Fung, S.

2004-01-01

The study of metal-semiconductor and metal-oxide-semiconductor systems with low energy positrons is made considerably easier if structures of millimeter dimension can be studied. For this reason the production of a positron beam of sub-millimeter dimension has been a long-term goal of the positron research group at the university of Hong Kong. The hybrid lens system employed consists of a standard Soa extraction lens in a magnetic field free region followed by a gridded Einzel lens that focuses positrons into a 100G magnetic funnel at an energy of 10keV for transportation to the target. Here we report on the present progress, by showing the capability of obtaining millimeter diameter focusing at a preliminary 7.5 kV beam energy. (orig.)

Diffusion of nanoparticles into the capsule and cortex of a crystalline lens

International Nuclear Information System (INIS)

Schachar, Ronald A; Chen Wei; Woo, Boon K; Pierscionek, Barbara K; Zhang, Xing; Ma, Lun

2008-01-01

The purpose of this study is to determine the ability of fluorescent nanoparticles to diffuse into a crystalline lens. Intact porcine lenses from five-month-old pigs, intact human lenses obtained from three donors aged 41, 42 and 45 years, and sections of human lens cortex obtained from four donors aged 11, 19, 32, and 34 years were incubated for 72 h at 7 deg. C in aqueous solutions of green (566 nm) and red (652 nm) fluorescent water soluble cadmium tellurium (CdTe) nanoparticles. As demonstrated by fluorescent and confocal microscopy, the CdTe nanoparticles diffused into the porcine and human lens capsule and into human cortical lens fibres; however, the nanoparticles did not pass through the intact lens capsule. Nanoparticles can be used as a method for studying intracellular structure and biochemical pathways within the lens capsule and cortical lens fibres to further understand cataractogenesis and may serve as a carrier for chemotherapeutic agents for the potential treatment of primary and secondary cataracts

Changes in lens stiffness due to capsular opacification in accommodative lens refilling

NARCIS (Netherlands)

Nibourg, Lisanne M.; Sharma, Prashant K.; van Kooten, Theo G.; Koopmans, Steven A.

Accommodation may be restored to presbyopic lenses by refilling the lens capsular bag with a soft polymer. After this accommodative lens refilling prevention of capsular opacification is a requirement, since capsular opacification leads to a decreased clarity of the refilled lens. It has been

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

GIS: a comprehensive source for protein structure similarities.

Science.gov (United States)

Guerler, Aysam; Knapp, Ernst-Walter

2010-07-01

A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. alpha-helices and beta-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10,000 protein domains yielding about 55 x 10(6) possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

Imaging off-plane shear waves with a two-dimensional phononic crystal lens

International Nuclear Information System (INIS)

Chiang Chenyu; Luan Pigang

2010-01-01

A two-dimensional flat phononic crystal (PC) lens for focusing off-plane shear waves is proposed. The lens consists of a triangular lattice hole-array, embedded in a solid matrix. The self-collimation effect is employed to guide the shear waves propagating through the lens along specific directions. The Dirichlet-to-Neumann maps (DtN) method is employed to calculate the band structure of the PC, which can avoid the problems of bad convergence and fake bands automatically in the void-solid PC structure. When the lens is illuminated by the off-plane shear waves emanating from a point source, a subwavelength image appears in the far-field zone. The imaging characteristics are investigated by calculating the displacement fields explicitly using the multiple scattering method, and the results are in good agreement with the ray-trace predictions. Our results may provide insights for designing new phononic devices.

Neural Networks for protein Structure Prediction

DEFF Research Database (Denmark)

Bohr, Henrik

1998-01-01

This is a review about neural network applications in bioinformatics. Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones...

FoxO3a Serves as a Biomarker of Oxidative Stress in Human Lens Epithelial Cells under Conditions of Hyperglycemia.

Directory of Open Access Journals (Sweden)

Ilangovan Raju

Full Text Available Forkhead box 'O' transcription factors (FoxOs are implicated in the pathogenesis of type2 diabetes and other metabolic diseases. Abnormal activity of FoxOs was reported in the glucose and insulin metabolism. Expression of FoxO proteins was reported in ocular tissues; however their function under hyperglycemic conditions was not examined.Human lens epithelial cell line was used to study the function of FoxO proteins. Immunofluorescence, flow cytometry and Western blotting were employed to detect the FoxO proteins under the conditions of hyperglycemia.In this study we examined the role of FoxO3a in hyperglycemia-induced oxidative stress in human lens epithelial cells. FoxO3a protein expression was elevated in a dose- and time-dependent fashion after high glucose treatment. Anti-oxidant defense mechanisms of the lens epithelial cells were diminished as evidenced from loss of mitochondrial membrane integrity and lowered MnSOD after 72 h treatment with high glucose. Taken together, FoxO3a acts as a sensitive indicator of oxidative stress and cell homeostasis in human lens epithelial cells during diabetic conditions.FoxO3a is an early stress response protein to glucose toxicity in diabetic conditions.

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

TU-E-201-03: Eye Lens Dosimetry in Radiotherapy Using Contact Lens-Shaped Applicator

Energy Technology Data Exchange (ETDEWEB)

Park, J. [Seoul National University Hospital (Korea, Republic of)

2015-06-15

Madan M. Rehani, Massachusetts General Hospital and Harvard Medical School, Boston Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionalists Radiation induced cataract is a major threat among staff working in interventional suites. Nearly 16 million interventional procedures are performed annually in USA. Recent studies by the principal investigator’s group, primarily among interventional cardiologists, on behalf of the International Atomic Energy Agency, show posterior subcapsular (PSC) changes in the eye lens in 38–53% of main operators and 21–45% of support staff. These changes have potential to lead to cataract in future years, as per information from A-Bomb survivors. The International Commission on Radiological Protection has reduced dose limit for staff by a factor of 7.5 (from 150 mSv/y to 20 mSv/y). With increasing emphasis on radiation induced cataracts and reduction in threshold dose for eye lens, there is a need to implement strategies for estimating eye lens dose. Unfortunately eye lens dosimetry is at infancy when it comes to routine application. Various approaches are being tried namely direct measurement using active or passive dosimeters kept close to eyes, retrospective estimations and lastly correlating patient dose in interventional procedures with staff eye dose. The talk will review all approaches available and ongoing active research in this area, as well as data from surveys done in Europe on status of eye dose monitoring in interventional radiology and nuclear medicine. The talk will provide update on how good is Hp(10) against Hp(3), estimations from CTDI values, Monte Carlo based simulations and current status of eye lens dosimetry in USA and Europe. The cataract risk among patients is in CT examinations of the head. Since radiation induced cataract predominantly occurs in posterior sub-capsular (PSC) region and is thus distinguishable from age or drug related cataracts and is also preventable, actions on

TU-E-201-03: Eye Lens Dosimetry in Radiotherapy Using Contact Lens-Shaped Applicator

International Nuclear Information System (INIS)

Park, J.

2015-01-01

Madan M. Rehani, Massachusetts General Hospital and Harvard Medical School, Boston Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionalists Radiation induced cataract is a major threat among staff working in interventional suites. Nearly 16 million interventional procedures are performed annually in USA. Recent studies by the principal investigator’s group, primarily among interventional cardiologists, on behalf of the International Atomic Energy Agency, show posterior subcapsular (PSC) changes in the eye lens in 38–53% of main operators and 21–45% of support staff. These changes have potential to lead to cataract in future years, as per information from A-Bomb survivors. The International Commission on Radiological Protection has reduced dose limit for staff by a factor of 7.5 (from 150 mSv/y to 20 mSv/y). With increasing emphasis on radiation induced cataracts and reduction in threshold dose for eye lens, there is a need to implement strategies for estimating eye lens dose. Unfortunately eye lens dosimetry is at infancy when it comes to routine application. Various approaches are being tried namely direct measurement using active or passive dosimeters kept close to eyes, retrospective estimations and lastly correlating patient dose in interventional procedures with staff eye dose. The talk will review all approaches available and ongoing active research in this area, as well as data from surveys done in Europe on status of eye dose monitoring in interventional radiology and nuclear medicine. The talk will provide update on how good is Hp(10) against Hp(3), estimations from CTDI values, Monte Carlo based simulations and current status of eye lens dosimetry in USA and Europe. The cataract risk among patients is in CT examinations of the head. Since radiation induced cataract predominantly occurs in posterior sub-capsular (PSC) region and is thus distinguishable from age or drug related cataracts and is also preventable, actions on

Contact Lens-Related Eye Infections

Science.gov (United States)

... Español Eye Health / Eye Health A-Z Contact Lens-Related Eye Infections Sections Contact Lens-Related Eye ... Six Steps to Avoid Contact Lens Infections Contact Lens-Related Eye Infections Leer en Español: Infecciones relacionadas ...

Structure based alignment and clustering of proteins (STRALCP)

Science.gov (United States)

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Validation-driven protein-structure improvement

NARCIS (Netherlands)

Touw, W.G.

2016-01-01

High-quality protein structure models are essential for many Life Science applications, such as protein engineering, molecular dynamics, drug design, and homology modelling. The WHAT_CHECK model validation project and the PDB_REDO model optimisation project have shown that many structure models in

Understanding Protein-Protein Interactions Using Local Structural Features

DEFF Research Database (Denmark)

Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

2013-01-01

Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation...... to score the likelihood of the interaction between two proteins and to develop a method for the prediction of PPIs. We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable...

Vortex gas lens

Science.gov (United States)

Bogdanoff, David W.; Berschauer, Andrew; Parker, Timothy W.; Vickers, Jesse E.

1989-01-01

A vortex gas lens concept is presented. Such a lens has a potential power density capability of 10 to the 9th - 10 to the 10th w/sq cm. An experimental prototype was constructed, and the divergence half angle of the exiting beam was measured as a function of the lens operating parameters. Reasonably good agreement is found between the experimental results and theoretical calculations. The expanded beam was observed to be steady, and no strong, potentially beam-degrading jets were found to issue from the ends of the lens. Estimates of random beam deflection angles to be expected due to boundary layer noise are presented; these angles are very small.

Efficient protein structure search using indexing methods.

Science.gov (United States)

Kim, Sungchul; Sael, Lee; Yu, Hwanjo

2013-01-01

Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

THE BOSS EMISSION-LINE LENS SURVEY. II. INVESTIGATING MASS-DENSITY PROFILE EVOLUTION IN THE SLACS+BELLS STRONG GRAVITATIONAL LENS SAMPLE

Energy Technology Data Exchange (ETDEWEB)

Bolton, Adam S.; Brownstein, Joel R.; Shu Yiping; Arneson, Ryan A. [Department of Physics and Astronomy, University of Utah, 115 South 1400 East, Salt Lake City, UT 84112 (United States); Kochanek, Christopher S. [Department of Astronomy and Center for Cosmology and Astroparticle Physics, Ohio State University, Columbus, OH 43210 (United States); Schlegel, David J. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Eisenstein, Daniel J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MS 20, Cambridge, MA 02138 (United States); Wake, David A. [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Connolly, Natalia [Department of Physics, Hamilton College, Clinton, NY 13323 (United States); Maraston, Claudia [Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX (United Kingdom); Weaver, Benjamin A., E-mail: bolton@astro.utah.edu [Center for Cosmology and Particle Physics, New York University, New York, NY 10003 (United States)

2012-09-20

We present an analysis of the evolution of the central mass-density profile of massive elliptical galaxies from the SLACS and BELLS strong gravitational lens samples over the redshift interval z Almost-Equal-To 0.1-0.6, based on the combination of strong-lensing aperture mass and stellar velocity-dispersion constraints. We find a significant trend toward steeper mass profiles (parameterized by the power-law density model with {rho}{proportional_to}r {sup -{gamma}}) at later cosmic times, with magnitude d < {gamma} > /dz = -0.60 {+-} 0.15. We show that the combined lens-galaxy sample is consistent with a non-evolving distribution of stellar velocity dispersions. Considering possible additional dependence of <{gamma} > on lens-galaxy stellar mass, effective radius, and Sersic index, we find marginal evidence for shallower mass profiles at higher masses and larger sizes, but with a significance that is subdominant to the redshift dependence. Using the results of published Monte Carlo simulations of spectroscopic lens surveys, we verify that our mass-profile evolution result cannot be explained by lensing selection biases as a function of redshift. Interpreted as a true evolutionary signal, our result suggests that major dry mergers involving off-axis trajectories play a significant role in the evolution of the average mass-density structure of massive early-type galaxies over the past 6 Gyr. We also consider an alternative non-evolutionary hypothesis based on variations in the strong-lensing measurement aperture with redshift, which would imply the detection of an 'inflection zone' marking the transition between the baryon-dominated and dark-matter halo-dominated regions of the lens galaxies. Further observations of the combined SLACS+BELLS sample can constrain this picture more precisely, and enable a more detailed investigation of the multivariate dependences of galaxy mass structure across cosmic time.

Vitamin C Degradation Products and Pathways in the Human Lens*

OpenAIRE

Nemet, Ina; Monnier, Vincent M.

2011-01-01

Vitamin C and its degradation products participate in chemical modifications of proteins in vivo through non-enzymatic glycation (Maillard reaction) and formation of different products called advanced glycation end products. Vitamin C levels are particularly high in selected tissues, such as lens, brain and adrenal gland, and its degradation products can inflict substantial protein damage via formation of advanced glycation end products. However, the pathways of in vivo vitamin C degradation ...

A 'periodic table' for protein structures.

Science.gov (United States)

Taylor, William R

2002-04-11

Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

Role of αA-crystallin-derived αA66-80 peptide in guinea pig lens crystallin aggregation and insolubilization.

Science.gov (United States)

Raju, Murugesan; Mooney, Brian P; Thakkar, Kavi M; Giblin, Frank J; Schey, Kevin L; Sharma, K Krishna

2015-03-01

Earlier we reported that low molecular weight (LMW) peptides accumulate in aging human lens tissue and that among the LMW peptides, the chaperone inhibitor peptide αA66-80, derived from α-crystallin protein, is one of the predominant peptides. We showed that in vitro αA66-80 induces protein aggregation. The current study was undertaken to determine whether LMW peptides are also present in guinea pig lens tissue subjected to hyperbaric oxygen (HBO) in vivo. The nuclear opacity induced by HBO in guinea pig lens is the closest animal model for studying age-related cataract formation in humans. A LMW peptide profile by mass spectrometry showed the presence of an increased amount of LMW peptides in HBO-treated guinea pig lenses compared to age-matched controls. Interestingly, the mass spectrometric data also showed that the chaperone inhibitor peptide αA66-80 accumulates in HBO-treated guinea pig lens. Following incubation of synthetic chaperone inhibitor peptide αA66-80 with α-crystallin from guinea pig lens extracts, we observed a decreased ability of α-crystallin to inhibit the amorphous aggregation of the target protein alcohol dehydrogenase and the formation of large light scattering aggregates, similar to those we have observed with human α-crystallin and αA66-80 peptide. Further, time-lapse recordings showed that a preformed complex of α-crystallin and αA66-80 attracted additional crystallin molecules to form even larger aggregates. These results demonstrate that LMW peptide-mediated cataract development in aged human lens and in HBO-induced lens opacity in the guinea pig may have common molecular pathways. Copyright © 2015 Elsevier Ltd. All rights reserved.

Primary anterior chamber intraocular lens for the treatment of severe crystalline lens subluxation.

Science.gov (United States)

Hoffman, Richard S; Fine, I Howard; Packer, Mark

2009-10-01

Subluxated cataractous and clear lenses are commonly treated by limbal or pars plana lensectomy followed by primary or secondary intraocular lens (IOL) implantation. Adjunctive capsular prosthetic devices have facilitated lens removal and IOL centration in these challenging cases but have also added complexity and potential complications to the procedure. Although crystalline lens extraction may be required to clear the visual axis in mild to moderate lens subluxations, we propose insertion of a primary anterior chamber IOL without lens extraction in severe subluxations when the eye is optically aphakic or can be made functionally aphakic following neodymium:YAG laser zonulysis. Two cases demonstrating this approach are presented.

Protein structure recognition: From eigenvector analysis to structural threading method

Science.gov (United States)

Cao, Haibo

In this work, we try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. We found a strong correlation between amino acid sequence and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, we give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part include discussions of interactions among amino acids residues, lattice HP model, and the designablity principle. In the second part, we try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in our eigenvector study of protein contact matrix. We believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, we discuss a threading method based on the correlation between amino acid sequence and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, we list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

Energy Technology Data Exchange (ETDEWEB)

Cao, Haibo [Iowa State Univ., Ames, IA (United States)

2003-01-01

In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

International Nuclear Information System (INIS)

Haibo Cao

2003-01-01

In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches

Structures composing protein domains.

Science.gov (United States)

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Current strategies for protein production and purification enabling membrane protein structural biology.

Science.gov (United States)

Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E; Liu, Xiang-Qin; Rainey, Jan K

2016-12-01

Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

An extended magnetic quadrupole lens for a high-resolution nuclear microprobe

Energy Technology Data Exchange (ETDEWEB)

Breese, M.B.H. E-mail: m.breese@surrey.ac.uk; Grime, G.W.; Linford, W.; Harold, M

1999-09-02

This paper describes the design requirements and initial performance of a new style of magnetic quadrupole lens for use in a high-resolution nuclear microprobe, which is presently being constructed in Oxford. Such a microprobe necessitates the use of a small image distance from the exit face of the final quadrupole lens to the image plane in order to produce a large demagnification. This means that the final lens should be as close to the sample chamber as possible. However, with conventional magnetic quadrupoles the current-carrying coils protrude by a typical distance of 10-20 mm beyond the pole face, thereby significantly limiting the minimum image distance. The approach taken here is to recess the coils into the body of the lens, so that they are almost flush with the pole pieces and lens yoke, enabling an image distance of 55 mm. Three-dimensional magnetic field calculations within this lens structure predict that the field in the extended pole piece 'nose' region is only slightly less than that in the main lens body. Experimental field profiles, measured using a Hall probe, are used to confirm these calculations.

An extended magnetic quadrupole lens for a high-resolution nuclear microprobe

International Nuclear Information System (INIS)

Breese, M.B.H.; Grime, G.W.; Linford, W.; Harold, M.

1999-01-01

This paper describes the design requirements and initial performance of a new style of magnetic quadrupole lens for use in a high-resolution nuclear microprobe, which is presently being constructed in Oxford. Such a microprobe necessitates the use of a small image distance from the exit face of the final quadrupole lens to the image plane in order to produce a large demagnification. This means that the final lens should be as close to the sample chamber as possible. However, with conventional magnetic quadrupoles the current-carrying coils protrude by a typical distance of 10-20 mm beyond the pole face, thereby significantly limiting the minimum image distance. The approach taken here is to recess the coils into the body of the lens, so that they are almost flush with the pole pieces and lens yoke, enabling an image distance of 55 mm. Three-dimensional magnetic field calculations within this lens structure predict that the field in the extended pole piece 'nose' region is only slightly less than that in the main lens body. Experimental field profiles, measured using a Hall probe, are used to confirm these calculations

Analysis of eye lens-specific genes in congenital hereditary cataracts and microphthalmia of the miniature schnauzer dog.

Science.gov (United States)

Zhang, R L; Samuelson, D A; Zhang, Z G; Reddy, V N; Shastry, B S

1991-08-01

The congenital hereditary cataracts and microphthalmia in the miniature schnauzer dog are inherited by an autosomal recessive mode. To understand the genetic basis of these diseases, the authors purified and analyzed leukocyte deoxyribonucleic acid (DNA) from affected and normal animals using a candidate gene approach. Because the genes that encode the lens-specific proteins, specifically, alpha, beta, and gamma crystallins and the membrane protein (MP26), are known to maintain the structure and function of the lens, the authors used complimentary DNA (cDNA) fragments that corresponded to the above genes to search for the mutations at their loci in the affected animals. They found no evidence of the gene deletion and rearrangement in any of the five loci. In addition, the hybridizable sequences of the dog DNA to the specific probes for the human chromosome 4 and 18 loci, which are reported to be involved in the abnormality of the human eye, seem to be unaffected. These data support the notion that the hereditary cataracts and microphthalmia in the dog may be associated with genes other than those reported for several animal systems.

Protein structure similarity from principle component correlation analysis

Directory of Open Access Journals (Sweden)

Chou James

2006-01-01

Full Text Available Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum

Probing the integrated Sachs-Wolfe effect using embedded lens models

Science.gov (United States)

Chen, B.; Kantowski, R.

2015-04-01

The photometry profile of the integrated Sachs-Wolfe (ISW) effect, recently obtained by the Planck consortium by stacking patches of cosmic microwave background (CMB) sky maps around a large number of cosmic voids, contains a cold ring at about half the void's effective radius surrounded by a hot ring near the void's boundary. The source of the temperature structure is assumed to be the ISW effect but the exact cause of the ringed structure is not currently well understood, particularly the outer hot ring. Numerical simulations have suggested that hot/cold ring structures can be produced by motions associated with nonlinear growths of cosmic structures whose gravitational potentials produce the ISW effect. We have recently developed the embedded lens theory and the Fermat potential formalism which can be used to model the ISW effect caused by intervening individual lens inhomogeneities evolving arbitrarily. This theory only requires knowledge of the void's projected mass profile as a function of the passing CMB photons' impact radius and the rate of change of that mass distribution at passage. We present two simple embedded void lens models with evolving mass densities and investigate the ISW effect caused by these lenses. Both models possess expanding mass shells which produce hot rings around central cold regions, consistent with the recent observations. By adding a small overdensity at the void's center we can produce the slight positive temperature excess hinted at in Planck's photometric results. We conclude that the embedded lens theory and the Fermat potential formalism is well suited for modeling the ISW effect.

Capsular 'pits' in the human lens.

OpenAIRE

Harris, M. L.; Brown, N. A.; Shun-Shin, G. A.; Smith, G. T.

1992-01-01

The lens capsule is an atypical basement membrane surrounding the lens epithelial cells and lens fibres which make up the remainder of the human lens. A seemingly unreported morphological change visible in the lens capsule with the biomicroscope is described.

Electrophoretic variation in low molecular weight lens crystallins from inbred strains of rats.

Science.gov (United States)

Donner, M E; Skow, L C; Kunz, H W; Gill, T J

1985-10-01

Analysis of rat lens soluble proteins by analytical isoelectric focusing detected two inherited electrophoretic differences in low molecular weight (LM) crystallins from inbred strains of rats (Rattus norvegicus). The polymorphic lens crystallins were shown to be similar to a genetically variant LM crystallin, LEN-1, previously described in mice (Mus musculus) and encoded on chromosome 1, at a locus linked to Pep-3 (dipeptidase). Linkage analysis demonstrated that the rat crystallin locus was loosely linked to Pep-3 at a recombination distance of 38 +/- 4.5 U. These data suggest the conservation of a large chromosomal region during the evolution of Rodentia and support the hypothesis that the gamma-crystallins are evolving more rapidly than alpha- or beta-crystallins.

Crosslinking and photoreaction of ozone-oxidized calf-lens alpha-crystallin

International Nuclear Information System (INIS)

Fujimori, E.

1982-01-01

Direct-photo-oxidation, singlet oxygen-oxidation, or photosensitized oxidation can modify lens crystallins, causing an increase in blue fluorescence and covalent crosslinking. A relationship between these changes has not been elucidated. We now report results from experiments with ozone oxidation. When calf-lens alpha-crystallin is treated with zone oxidation. When calf-lens alpha-crystallin is treated with ozone, new absorption, fluorescence, and phosphorescence, which are characteristic of the oxidized product of tryptophan (N-formylkynurenine), appear at 320, 435, and 445 nm, respectively. In addition, in this ozonization of alpha-crystallin, its polypeptides are crosslinked by nondisulfide bonds. Irradiation of ozone-treated alpha-crystallin with near-ultraviolet (365 nm) light increases crosslinking and reduces the 320 nm absorbance with a concomitant appearance of a new absorption at about 420 nm. This photoproduct exhibits an intense fluorescence around 450 nm and a weak phosphorescence at 510 nm, with excitation peaks at 400, 415, and 422 nm. These findings are essentially the same as those observed in photo-oxidized alpha-crystallin, suggesting the involvement of the same tryptophan oxidized product in the modification of the lens protein

SDSL-ESR-based protein structure characterization

NARCIS (Netherlands)

Strancar, J.; Kavalenka, A.A.; Urbancic, I.; Ljubetic, A.; Hemminga, M.A.

2010-01-01

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be

A high excitation magnetic quadrupole lens quadruplet incorporating a single octupole lens for a low spherical aberration probe forming lens system

Science.gov (United States)

Dou, Yanxin; Jamieson, David N.; Liu, Jianli; Li, Liyi

2018-03-01

This paper describes the design of a new probe forming lens system consisting of a high excitation magnetic quadrupole lens quadruplet that incorporates a single magnetic octupole lens. This system achieves both a high demagnification and a low spherical aberration compared to conventional high excitation systems and is intended for deployment for the Harbin 300 MeV proton microprobe for applications in space science and ion beam therapy. This relative simplicity of the ion optical design to include a single octupole lens minimizes the risks associated with the constructional and operational precision usually needed for the probe forming lens system and this system could also be deployed in microprobe systems that operate with less magnetically rigid ions. The design of the new system is validated with reference to two independent ion optical computer codes.

The effect of pipecol angles for the magnetic electron lens on the aberration coefficients

International Nuclear Information System (INIS)

Al-Khshab, A. M.; Al-Khshab, A. H.

1997-01-01

The symmetric mag etic objective lens of great importance for the electronic microscopes intended for hi g resolution. Such lens is determined, not only by its geometries structure and shape parameters, but also by the influence of the variation of the pole piece angles. the results show that the Objective lens having the pole piece angle of 55 a has a considerable effect on the electron optical Properties. When this pole piece is appropriately and highly saturated, the lens possesses low spherical and chromatic aberration coefficients. This hind of pole piece lens leads to more favourable design than other lenses. (authors). 14 refs., 7 figs.1 table

Development of a 3D finite element model of lens microcirculation

Directory of Open Access Journals (Sweden)

Vaghefi Ehsan

2012-09-01

Full Text Available Abstract Background It has been proposed that in the absence of a blood supply, the ocular lens operates an internal microcirculation system. This system delivers nutrients, removes waste products and maintains ionic homeostasis in the lens. The microcirculation is generated by spatial differences in membrane transport properties; and previously has been modelled by an equivalent electrical circuit and solved analytically. While effective, this approach did not fully account for all the anatomical and functional complexities of the lens. To encapsulate these complexities we have created a 3D finite element computer model of the lens. Methods Initially, we created an anatomically-correct representative mesh of the lens. We then implemented the Stokes and advective Nernst-Plank equations, in order to model the water and ion fluxes respectively. Next we complemented the model with experimentally-measured surface ionic concentrations as boundary conditions and solved it. Results Our model calculated the standing ionic concentrations and electrical potential gradients in the lens. Furthermore, it generated vector maps of intra- and extracellular space ion and water fluxes that are proposed to circulate throughout the lens. These fields have only been measured on the surface of the lens and our calculations are the first 3D representation of their direction and magnitude in the lens. Conclusion Values for steady state standing fields for concentration and electrical potential plus ionic and fluid fluxes calculated by our model exhibited broad agreement with observed experimental values. Our model of lens function represents a platform to integrate new experimental data as they emerge and assist us to understand how the integrated structure and function of the lens contributes to the maintenance of its transparency.

Objective lens

Science.gov (United States)

Olczak, Eugene G. (Inventor)

2011-01-01

An objective lens and a method for using same. The objective lens has a first end, a second end, and a plurality of optical elements. The optical elements are positioned between the first end and the second end and are at least substantially symmetric about a plane centered between the first end and the second end.

Contact Lens Care

Science.gov (United States)

... Consumers Consumer Information by Audience For Women Contact Lens Care Share Tweet Linkedin Pin it More sharing ... www.fda.gov/medwatch Learn More about Contact Lens Care Other Tips on Contact Lenses Decorative Contact ...

The tumor suppressor gene Trp53 protects the mouse lens against posterior subcapsular cataracts and the BMP receptor Acvr1 acts as a tumor suppressor in the lens

Directory of Open Access Journals (Sweden)

Luke A. Wiley

2011-07-01

We previously found that lenses lacking the Acvr1 gene, which encodes a bone morphogenetic protein (BMP receptor, had abnormal proliferation and cell death in epithelial and cortical fiber cells. We tested whether the tumor suppressor protein p53 (encoded by Trp53 affected this phenotype. Acvr1 conditional knockout (Acvr1CKO mouse fiber cells had increased numbers of nuclei that stained for p53 phosphorylated on serine 15, an indicator of p53 stabilization and activation. Deletion of Trp53 rescued the Acvr1CKO cell death phenotype in embryos and reduced Acvr1-dependent apoptosis in postnatal lenses. However, deletion of Trp53 alone increased the number of fiber cells that failed to withdraw from the cell cycle. Trp53CKO and Acvr1;Trp53DCKO (double conditional knockout, but not Acvr1CKO, lenses developed abnormal collections of cells at the posterior of the lens that resembled posterior subcapsular cataracts. Cells from human posterior subcapsular cataracts had morphological and molecular characteristics similar to the cells at the posterior of mouse lenses lacking Trp53. In Trp53CKO lenses, cells in the posterior plaques did not proliferate but, in Acvr1;Trp53DCKO lenses, many cells in the posterior plaques continued to proliferate, eventually forming vascularized tumor-like masses at the posterior of the lens. We conclude that p53 protects the lens against posterior subcapsular cataract formation by suppressing the proliferation of fiber cells and promoting the death of any fiber cells that enter the cell cycle. Acvr1 acts as a tumor suppressor in the lens. Enhancing p53 function in the lens could contribute to the prevention of steroid- and radiation-induced posterior subcapsular cataracts.

Changes in the distribution of lens calcium during development of x-ray cataract

International Nuclear Information System (INIS)

Hightower, K.R.; Giblin, F.J.; Reddy, V.N.

1983-01-01

The present study was designed to examine the possible role of calcium in the opacification of x-ray-induced cataract in rabbit. The results demonstrate that the concentration of calcium in x-rayed lenses, just prior to lens hydration (7.5 weeks postirradiation), was twice that present in contralateral control lenses. At this stage of immature cataract, the lens nucleus remained transparent and maintained a normal level of calcium, but the lens cortex, containing regions of subcapsular opacification, accumulated a level of calcium that was twice that of the control. In the completely opaque mature cataract, (8-9 weeks post x-ray), both the cortex and nucleus had gained significant amounts of calcium. As the concentration of total calcium increased in the immature x-ray cataract, the amount of the cation bound to membranes and insoluble proteins of the cytosol also increased comparably. However, the relative proportion of calcium in the various fractions remained unaltered in the immature cataract; in both control lenses and immature cataracts, 20% of the total calcium remained in the membrane pellet and 70% was located in the soluble protein fraction. Only in the mature stage of cataract was a shift in the distribution of calcium apparent, as the proportion of calcium in the soluble protein fraction increased to 90%. Although only 7% of the total calcium in a mature cataract was bound to membrane, the amount represented a fivefold increase over the control. The results of this study demonstrate that an elevation in lens calcium accompanies the opacification process in x-ray cataract. The work also suggests that changes in calcium levels are not likely to result from inactivation of Ca-ATPase

Integrated Lens Antennas for Multi-Pixel Receivers

Science.gov (United States)

Lee, Choonsup; Chattopadhyay, Goutam

2011-01-01

Future astrophysics and planetary experiments are expected to require large focal plane arrays with thousands of detectors. Feedhorns have excellent performance, but their mass, size, fabrication challenges, and expense become prohibitive for very large focal plane arrays. Most planar antenna designs produce broad beam patterns, and therefore require additional elements for efficient coupling to the telescope optics, such as substrate lenses or micromachined horns. An antenna array with integrated silicon microlenses that can be fabricated photolithographically effectively addresses these issues. This approach eliminates manual assembly of arrays of lenses and reduces assembly errors and tolerances. Moreover, an antenna array without metallic horns will reduce mass of any planetary instrument significantly. The design has a monolithic array of lens-coupled, leaky-wave antennas operating in the millimeter- and submillimeter-wave frequencies. Electromagnetic simulations show that the electromagnetic fields in such lens-coupled antennas are mostly confined in approximately 12 15 . This means that one needs to design a small-angle sector lens that is much easier to fabricate using standard lithographic techniques, instead of a full hyper-hemispherical lens. Moreover, this small-angle sector lens can be easily integrated with the antennas in an array for multi-pixel imager and receiver implementation. The leaky antenna is designed using double-slot irises and fed with TE10 waveguide mode. The lens implementation starts with a silicon substrate. Photoresist with appropriate thickness (optimized for the lens size) is spun on the substrate and then reflowed to get the desired lens structure. An antenna array integrated with individual lenses for higher directivity and excellent beam profile will go a long way in realizing multi-pixel arrays and imagers. This technology will enable a new generation of compact, low-mass, and highly efficient antenna arrays for use in multi

Amino acid code of protein secondary structure.

Science.gov (United States)

Shestopalov, B V

2003-01-01

The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

X-ray effects of lens DNA-implications of superoxide (O2.-)

International Nuclear Information System (INIS)

Srivastava, V.K.; Richards, R.D.; Varma, S.D.

1983-01-01

The photocemical generation of superoxide (O 2 .-) during in vitro exposure of bovine lenses induced damage in the structure of lens DNA as indicated by hyperchromicity and Tm measurements. The damage in lens DNA was significantly protected by the inclusion of superoxide dismutase (SOD), glutathione (GSH) and ascorbate in the incubation medium before X-ray exposure. The protection by SOD, GSH and ascorbate occurred due to their interaction with O 2 .- radicals. These results thus indicate the deleterious effect of O 2 .- in lens physiology and the protective role of such compounds against radiation damage. (author)

Electro-optical characteristics of a liquid crystal lens with polymer network

International Nuclear Information System (INIS)

Bielyikh, S.P.; Subota, S.L.; Reshetnyak, V.Y.; Galstian, T.

2010-01-01

We study a tunable-focus lens in which the key element is a gradient-polymer-stabilized liquid crystal (G-PSLC) structure. In this paper, we further develop the theoretical model, that describes the dependence of the G-PSLC lens' focal length on the applied voltage and presents a theoretical study of lens aberrations. According to Fermat's principle, we minimize the optical path of a test light beam and calculate the angles of a ray exiting from the cell. Using these results, the lateral and longitudinal aberrations are estimated. The obtained results can be used to optimize the G-PSLC lenses.

Oxygen transport through soft contact lens and cornea: Lens characterization and metabolic modeling

Science.gov (United States)

Chhabra, Mahendra

The human cornea requires oxygen to sustain metabolic processes critical for its normal functioning. Any restriction to corneal oxygen supply from the external environment (e.g., by wearing a low oxygen-permeability contact lens) can lead to hypoxia, which may cause corneal edema (swelling), limbal hyperemia, neovascularization, and corneal acidosis. The need for adequate oxygen to the cornea is a major driving force for research and development of hypertransmissible soft contact lenses (SCLs). Currently, there is no standard technique for measuring oxygen permeability (Dk) of hypertransmissible silicone-hydrogel SCLs. In this work, an electrochemistry-based polarographic apparatus was designed, built, and operated to measure oxygen permeability in hypertransmissible SCLs. Unlike conventional methods where a range of lens thickness is needed for determining oxygen permeabilities of SCLs, this apparatus requires only a single lens thickness. The single-lens permeameter provides a reliable, efficient, and economic tool for measuring oxygen permeabilities of commercial hypertransmissible SCLs. The single-lens permeameter measures not only the product Dk, but, following modification, it measures separately diffusivity, D, and solubility, k, of oxygen in hypertransmissible SCLs. These properties are critical for designing better lens materials that ensure sufficient oxygen supply to the cornea. Metabolism of oxygen in the cornea is influenced by contact-lens-induced hypoxia, diseases such as diabetes, surgery, and drug treatment, Thus, estimation of the in-vivo corneal oxygen consumption rate is essential for gauging adequate oxygen supply to the cornea. Therefore, we have developed an unsteady-state reactive-diffusion model for the cornea-contact-lens system to determine in-vivo human corneal oxygen-consumption rate. Finally, a metabolic model was developed to determine the relation between contact-lens oxygen transmissibility (Dk/L) and corneal oxygen deficiency. A

Crystal Structure of Chicken γS-Crystallin Reveals Lattice Contacts with Implications for Function in the Lens and the Evolution of the βγ-Crystallins.

Science.gov (United States)

Sagar, Vatsala; Chaturvedi, Sumit K; Schuck, Peter; Wistow, Graeme

2017-07-05

Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16 chicken γS crystallized avidly while the Q16 mutant did not. The X-ray structure for chicken γS at 2.3 Å resolution shows the canonical structure of the superfamily plus a well-ordered N arm aligned with a β sheet of a neighboring N domain. L16 is also in a lattice contact, partially shielded from solvent. Unexpectedly, the major lattice contact matches a conserved interface (QR) in the multimeric β-crystallins. QR shows little conservation of residue contacts, except for one between symmetry-related tyrosines, but molecular dipoles for the proteins with QR show striking similarities while other γ-crystallins differ. In γS, QR has few hydrophobic contacts and features a thin layer of tightly bound water. The free energy of QR is slightly repulsive and analytical ultracentrifugation confirms no dimerization in solution. The lattice contacts suggest how γ-crystallins allow close packing without aggregation in the crowded environment of the lens. Published by Elsevier Ltd.

Crystalline lens power and refractive error.

Science.gov (United States)

Iribarren, Rafael; Morgan, Ian G; Nangia, Vinay; Jonas, Jost B

2012-02-01

To study the relationships between the refractive power of the crystalline lens, overall refractive error of the eye, and degree of nuclear cataract. All phakic participants of the population-based Central India Eye and Medical Study with an age of 50+ years were included. Calculation of the refractive lens power was based on distance noncycloplegic refractive error, corneal refractive power, anterior chamber depth, lens thickness, and axial length according to Bennett's formula. The study included 1885 subjects. Mean refractive lens power was 25.5 ± 3.0 D (range, 13.9-36.6). After adjustment for age and sex, the standardized correlation coefficients (β) of the association with the ocular refractive error were highest for crystalline lens power (β = -0.41; P lens opacity grade (β = -0.42; P lens power (β = -0.95), lower corneal refractive power (β = -0.76), higher lens thickness (β = 0.30), deeper anterior chamber (β = 0.28), and less marked nuclear lens opacity (β = -0.05). Lens thickness was significantly lower in eyes with greater nuclear opacity. Variations in refractive error in adults aged 50+ years were mostly influenced by variations in axial length and in crystalline lens refractive power, followed by variations in corneal refractive power, and, to a minor degree, by variations in lens thickness and anterior chamber depth.

Minimum Lens Size Supporting the Leaky-Wave Nature of Slit Dipole Antenna at Terahertz Frequency

Directory of Open Access Journals (Sweden)

Niamat Hussain

2016-01-01

Full Text Available We designed a slit dipole antenna backed by an extended hemispherical silicon lens and investigated the minimum lens size in which the slit dipole antenna works as a leaky-wave antenna. The slit dipole antenna consists of a planar feeding structure, which is a center-fed and open-ended slot line. A slit dipole antenna backed by an extended hemispherical silicon lens is investigated over a frequency range from 0.2 to 0.4 THz with the center frequency at 0.3 THz. The numerical results show that the antenna gain responses exhibited an increased level of sensitivity to the lens size and increased linearly with increasing lens radius. The lens with the radius of 1.2λo is found to be the best possible minimum lens size for a slit dipole antenna on an extended hemispherical silicon lens.

Time-specific blockade of PDGFR with Imatinib (Glivec®) causes cataract and disruption of lens fiber cells in neonatal mice.

Science.gov (United States)

Zhou, Yin-Pin; He, Yang-Tao; Chen, Cheng-Li; Ji, Jun; Niu, Jian-Qin; Wang, Han-Zhi; Li, Shi-Feng; Huang, Lan; Mei, Feng

2011-03-01

This study aimed at investigating the response of lens epithelial cells in postnatal mice to Imatinib (Glivec®, a potent inhibitor of platelet-derived growth factor receptor (PDGFR)) treatment. Mouse eyes were sampled 10 days after administration of Imatinib (0.5 mg·g(-1)·day(-1)) for 3 days, at either 7, 14, or 21 days postpartum. Structural changes of lens were revealed by routine H.E. staining. Levels of proliferation and apoptosis were revealed by BrdU incorporation and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, respectively, and immunofluorescent staining with anti-PDGFRα antibody was carried out on the sections of eyeball. PDGFRα and p-PDGFRαprotein levels were evaluated by Western blot. Our results indicated that administration of Imatinib led to blockade of PDGFR signaling. Formation of cataracts was found only in those mice where treatment started from 7 days postpartum (P7), but was not observed in those samples from P14 nor P21. Fiber cells were disorganized in cataract lens core as observed histologically, and migration of epithelial cells was also inhibited. No apoptosis was detected with the TUNEL method. Our results indicated blockade of PDGFR at the neonatal stage (P7) would lead to cataracts and lens fiber cells disorganization, suggesting that PDGFR signaling plays a time-specific and crucial role in the postnatal development of lens in the mouse, and also may provide a new approach to produce a congenital cataract animal model.

Development of a Laue lens for nuclear astrophysics

International Nuclear Information System (INIS)

Barriere, N.

2008-04-01

The Laue lenses we study focuses in the domain of 0.1-1 MeV thanks to Bragg diffraction in the volume of a large number of small crystal tiles. The focal length of a typical Laue lens system is of the order of 100 m. This requirement calls for two formation flying satellites maintaining lens and detector at the focal distance. The major breakthrough of Laue lenses is to decouple collecting area from detector area. Concentrating a signal from the large area of a Laue lens onto a small focal spot dramatically increases the signal over background ratio with respect to present technologies. Here is the reason for the long awaited leap in sensitivity. The objective of the present thesis was to improve the concept, finding viable technical solutions towards a future space mission. Two aspects of the lens development have been highlighted in this thesis: the first one is an analytical model of the lens that is used to calculate and improve the performance of a certain configuration, the second aspect concerns the search and the characterization of diffracting media of interest. The lens model developed relies on a fast semi-analytical simulation library, permitting to build several design- and optimisation-tools. For the configuration of a given lens, this code computes the resulting effective area and point spread function in a handful of seconds. The model helps finding lens configurations (mass, pack ratio of the lens rings,...) which are automatically refined to match with effective area and energy coverage constraints. These tools have been used to investigate various design aspects, such as the influence of focal length, size, mosaic spread, structure and materials of crystals, etc... The central evaluation criterion in the model is a figure of merit, based on the compactness of the focal spot and the intensity of the collected signal. The second part of this work addresses the actual search and characterization of crystals potentially interesting for Laue lenses

Overcoming barriers to membrane protein structure determination.

Science.gov (United States)

Bill, Roslyn M; Henderson, Peter J F; Iwata, So; Kunji, Edmund R S; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G; Vogel, Horst

2011-04-01

After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.

Characteristics of the thick, compound refractive lens

International Nuclear Information System (INIS)

Pantell, Richard H.; Feinstein, Joseph; Beguiristain, H. Raul; Piestrup, Melvin A.; Gary, Charles K.; Cremer, Jay T.

2003-01-01

A compound refractive lens (CRL), consisting of a series of N closely spaced lens elements each of which contributes a small fraction of the total focusing, can be used to focus x rays or neutrons. The thickness of a CRL can be comparable to its focal length, whereupon a thick-lens analysis must be performed. In contrast with the conventional optical lens, where the ray inside the lens follows a straight line, the ray inside the CRL is continually changing direction because of the multiple refracting surfaces. Thus the matrix representation for the thick CRL is quite different from that for the thick optical lens. Principal planes can be defined such that the thick-lens matrix can be converted to that of a thin lens. For a thick lens the focal length is greater than for a thin lens with the same lens curvature, but this lengthening effect is less for the CRL than for the conventional optical lens

A planar lens based on the electrowetting of two immiscible liquids

International Nuclear Information System (INIS)

Liu Chaoxuan; Park, Jihwan; Choi, Jin-Woo

2008-01-01

This paper reports the development and characterization of a planar liquid lens based on electrowetting. The working concept of electrowetting two immiscible liquids is demonstrated with measurement and characterization of contact angles with regard to externally applied electric voltages. Consequently, a planar liquid lens is designed and implemented based on this competitive electrowetting. A droplet of silicone oil confined in an aqueous solution (1% KCl) works as a liquid lens. Electrowetting then controls the shape of the confined silicone oil and the focal length of the liquid lens varies depending upon an applied dc voltage. A unique feature of this lens design is the double-ring planar electrodes beneath the hydrophobic substrate. While an outer ring electrode provides an initial boundary for the silicone oil droplet, an inner ring works as the actuation electrode for the lens. Further, the planar electrodes, instead of vertical or out-of-plane wall electrodes, facilitate the integration of liquid lenses into microfluidic systems. With the voltage applied in the range of 50–250 V, the confined silicone oil droplet changed its shape and the optical magnification of a 3 mm-diameter liquid lens was clearly demonstrated. Moreover, focal lengths of liquid lenses with diameters of 2 mm, 3 mm and 4 mm were characterized, respectively. The obtained results suggest that a larger lens diameter yields a longer focal length and a wider range of focal length change in response to voltage. The demonstrated liquid lens has a simple structure and is easy to fabricate

Quality assessment of protein model-structures based on structural and functional similarities.

Science.gov (United States)

Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

2012-09-21

Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and

The ring cycle: an iterative lens reconstruction technique applied to MG1131 + 0456

International Nuclear Information System (INIS)

Kochanek, C.S.; Blandford, R.D.; Lawrence, C.R.; Narayan, R.

1989-01-01

A new technique is described for the analysis of well-resolved gravitational lens images. This method allows us to solve for the brightness distribution of the unlensed source as well as a parametrized model of the lens. Our algorithm computes a figure of merit for a lens model based on the scatter in the surface brightnesses of image elements that, according to the model, come from the same source element. Minimization of the figure of merit leads to an optimum solution for the source and the lens. We present a successful application of the method to VLA maps of the 'Einstein ring' radio source MG1131 + 0456 observed by previous authors. The inversion gives a normal galaxy-like elliptical potential for the lens and an ordinary double-lobed structure for the background radio source. (author)

TU-E-201-01: Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionists

Energy Technology Data Exchange (ETDEWEB)

Rehani, M. [Massachusetts General Hospital (United States)

2015-06-15

Madan M. Rehani, Massachusetts General Hospital and Harvard Medical School, Boston Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionalists Radiation induced cataract is a major threat among staff working in interventional suites. Nearly 16 million interventional procedures are performed annually in USA. Recent studies by the principal investigator’s group, primarily among interventional cardiologists, on behalf of the International Atomic Energy Agency, show posterior subcapsular (PSC) changes in the eye lens in 38–53% of main operators and 21–45% of support staff. These changes have potential to lead to cataract in future years, as per information from A-Bomb survivors. The International Commission on Radiological Protection has reduced dose limit for staff by a factor of 7.5 (from 150 mSv/y to 20 mSv/y). With increasing emphasis on radiation induced cataracts and reduction in threshold dose for eye lens, there is a need to implement strategies for estimating eye lens dose. Unfortunately eye lens dosimetry is at infancy when it comes to routine application. Various approaches are being tried namely direct measurement using active or passive dosimeters kept close to eyes, retrospective estimations and lastly correlating patient dose in interventional procedures with staff eye dose. The talk will review all approaches available and ongoing active research in this area, as well as data from surveys done in Europe on status of eye dose monitoring in interventional radiology and nuclear medicine. The talk will provide update on how good is Hp(10) against Hp(3), estimations from CTDI values, Monte Carlo based simulations and current status of eye lens dosimetry in USA and Europe. The cataract risk among patients is in CT examinations of the head. Since radiation induced cataract predominantly occurs in posterior sub-capsular (PSC) region and is thus distinguishable from age or drug related cataracts and is also preventable, actions on

TU-E-201-01: Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionists

International Nuclear Information System (INIS)

Rehani, M.

2015-01-01

Madan M. Rehani, Massachusetts General Hospital and Harvard Medical School, Boston Methods for Eye Lens Dosimetry and Studies On Lens Opacities with Interventionalists Radiation induced cataract is a major threat among staff working in interventional suites. Nearly 16 million interventional procedures are performed annually in USA. Recent studies by the principal investigator’s group, primarily among interventional cardiologists, on behalf of the International Atomic Energy Agency, show posterior subcapsular (PSC) changes in the eye lens in 38–53% of main operators and 21–45% of support staff. These changes have potential to lead to cataract in future years, as per information from A-Bomb survivors. The International Commission on Radiological Protection has reduced dose limit for staff by a factor of 7.5 (from 150 mSv/y to 20 mSv/y). With increasing emphasis on radiation induced cataracts and reduction in threshold dose for eye lens, there is a need to implement strategies for estimating eye lens dose. Unfortunately eye lens dosimetry is at infancy when it comes to routine application. Various approaches are being tried namely direct measurement using active or passive dosimeters kept close to eyes, retrospective estimations and lastly correlating patient dose in interventional procedures with staff eye dose. The talk will review all approaches available and ongoing active research in this area, as well as data from surveys done in Europe on status of eye dose monitoring in interventional radiology and nuclear medicine. The talk will provide update on how good is Hp(10) against Hp(3), estimations from CTDI values, Monte Carlo based simulations and current status of eye lens dosimetry in USA and Europe. The cataract risk among patients is in CT examinations of the head. Since radiation induced cataract predominantly occurs in posterior sub-capsular (PSC) region and is thus distinguishable from age or drug related cataracts and is also preventable, actions on

Wind lens technology and its application to wind and water turbine and beyond

Directory of Open Access Journals (Sweden)

Ohya Yuji

2017-01-01

Full Text Available Wind lens is a new type of wind power system consisting of a simple brimmed ring structure that surrounds the rotor causing greater wind to pass through the turbine. As a consequence, the turbine's efficiency of capturing energy from the wind gets dramatically increased. A Wind lens turbine can generate 2–5 times the power of an existing wind turbine given at the same rotor diameter and incoming wind speed. This fluid dynamical effect is also effective in the water. We have developed 1–3 kW Wind lens turbines and a 100 kW Wind lens turbine. In addition to the enhanced output power, Wind lens turbine is quiet. The technology is now used in an offshore experiment with a hexagonal float 18 meters in diameter set off the coast of Hakata Bay in Fukuoka City. Moreover, we are now pursuing larger size Wind lens turbines through multi-rotor design consisting of multiple Wind lens turbines in a same vertical plane to embody larger total power output.

DISSECTING THE GRAVITATIONAL LENS B1608+656. I. LENS POTENTIAL RECONSTRUCTION

NARCIS (Netherlands)

Suyu, S. H.; Marshall, P. J.; Blandford, R. D.; Fassnacht, C. D.; Koopmans, L. V. E.; McKean, J. P.; Treu, T.

2009-01-01

Strong gravitational lensing is a powerful technique for probing galaxy mass distributions and for measuring cosmological parameters. Lens systems with extended source-intensity distributions are particularly useful for this purpose since they provide additional constraints on the lens potential (

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

KAUST Repository

Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

2016-01-01

Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment

Structural determination of intact proteins using mass spectrometry

Science.gov (United States)

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

Nonlinear laser pulse response in a crystalline lens.

Science.gov (United States)

Sharma, R P; Gupta, Pradeep Kumar; Singh, Ram Kishor; Strickland, D

2016-04-01

The propagation characteristics of a spatial Gaussian laser pulse have been studied inside a gradient-index structured crystalline lens with constant-density plasma generated by the laser-tissue interaction. The propagation of the laser pulse is affected by the nonlinearities introduced by the generated plasma inside the crystalline lens. Owing to the movement of plasma species from a higher- to a lower-temperature region, an increase in the refractive index occurs that causes the focusing of the laser pulse. In this study, extended paraxial approximation has been applied to take into account the evolution of the radial profile of the Gaussian laser pulse. To examine the propagation characteristics, variation of the beam width parameter has been observed as a function of the laser power and initial beam radius. The cavitation bubble formation, which plays an important role in the restoration of the elasticity of the crystalline lens, has been investigated.

Simulation of an Aspheric Glass Lens Forming Behavior in Progressive GMP Process

International Nuclear Information System (INIS)

Chang, Sung Ho; Lee, Young Min; Kang, Jeong Jin; Hong, Seok Kwan; Shin, Gwang Ho; Heo, Young Moo; Jung, Tae Sung

2007-01-01

Recently, GMP(Glass Molding Press) process is mainly used to produce aspheric glass lenses. Because glass lens is heated at high temperature above Tg (Transformation Temperature) for forming the glass, the quality of aspheric glass lens is deteriorated by residual stresses which are generated in a aspheric glass lens after forming. In this study, as a fundamental study to develop the mold for progressive GMP process, we conducted a aspheric glass lens forming simulation. Prior to a aspheric glass lens forming simulation, compression and thermal conductivity tests were carried out to obtain mechanical and thermal properties of K-PBK40 which is newly developed material for precision molding, and flow characteristics of K-PBK40 were obtained at high temperature. Then, using the flow characteristics obtained, compression simulation was carried out and compared with the experimental result for the purpose of verifying the obtained flow characteristics. Finally, a glass lens press simulation in progressive GMP process was carried out and we could forecast the shape of deformed glass lenses and residual stresses contribution in the structure of deformed glass lenses after forming

Structural basis for target protein recognition by the protein disulfide reductase thioredoxin

DEFF Research Database (Denmark)

Maeda, Kenji; Hägglund, Per; Finnie, Christine

2006-01-01

Thioredoxin is ubiquitous and regulates various target proteins through disulfide bond reduction. We report the structure of thioredoxin (HvTrxh2 from barley) in a reaction intermediate complex with a protein substrate, barley alpha-amylase/subtilisin inhibitor (BASI). The crystal structure...... of this mixed disulfide shows a conserved hydrophobic motif in thioredoxin interacting with a sequence of residues from BASI through van der Waals contacts and backbone-backbone hydrogen bonds. The observed structural complementarity suggests that the recognition of features around protein disulfides plays...... a major role in the specificity and protein disulfide reductase activity of thioredoxin. This novel insight into the function of thioredoxin constitutes a basis for comprehensive understanding of its biological role. Moreover, comparison with structurally related proteins shows that thioredoxin shares...

Protein structure: geometry, topology and classification

Energy Technology Data Exchange (ETDEWEB)

Taylor, William R.; May, Alex C.W.; Brown, Nigel P.; Aszodi, Andras [Division of Mathematical Biology, National Institute for Medical Research, London (United Kingdom)

2001-04-01

The structural principals of proteins are reviewed and analysed from a geometric perspective with a view to revealing the underlying regularities in their construction. Computer methods for the automatic comparison and classification of these structures are then reviewed with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of the classification of proteins, more abstract geometric and topological representations are explored, including the occurrence of knotted topologies. The review concludes with a consideration of the origin of higher-level symmetries in protein structure. (author)

Optimization of a multilayer Laue lens system for a hard x-ray nanoprobe

International Nuclear Information System (INIS)

Jiang, Hui; Wang, Hua; Mao, Chengwen; Li, Aiguo; He, Yan; Dong, Zhaohui; Zheng, Yi

2014-01-01

Detailed designs of a multilayer Laue lens system for a hard x-ray nanoprobe, including flat and wedged types, are presented, to realize nanoscale point focus and high diffraction efficiency simultaneously. The difficulty of movement and alignment for lens, aperture and sample are considered in the optimization process. Considering the practical requirements of future experiments, the features of the beamline and the structural imperfections, the working energy range, the beam vibration and structural errors are estimated and discussed. (paper)

Use of designed sequences in protein structure recognition.

Science.gov (United States)

Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

2018-05-09

Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

PDB2CD visualises dynamics within protein structures.

Science.gov (United States)

Janes, Robert W

2017-10-01

Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

Science.gov (United States)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Intraocular lens fabrication

Energy Technology Data Exchange (ETDEWEB)

Salazar, Mike A. (Albuquerque, NM); Foreman, Larry R. (Los Alamos, NM)

1997-01-01

This invention describes a method for fabricating an intraocular lens made rom clear Teflon.TM., Mylar.TM., or other thermoplastic material having a thickness of about 0.025 millimeters. These plastic materials are thermoformable and biocompatable with the human eye. The two shaped lenses are bonded together with a variety of procedures which may include thermosetting and solvent based adhesives, laser and impulse welding, and ultrasonic bonding. The fill tube, which is used to inject a refractive filling material is formed with the lens so as not to damage the lens shape. A hypodermic tube may be included inside the fill tube.

Escape from X-ray-induced arrest for lens cells stimulated from quiescence: time relationship to RNA, protein, and DNA synthesis

International Nuclear Information System (INIS)

Lindgren, A.L.; Miller, R.C.; Guernsey, D.L.; Riley, E.F.

1988-01-01

Quiescent cells of the central zone region of the rat lens epithelium were stimulated to enter the proliferation cycle by wounding. RNA synthesis and a corresponding increase in poly(A)+/total RNA reached a peak by Hour 4. Cells progressed into the G1B compartment by Hour 10. A rise in protein synthesis began at Hour 8, and onset of DNA synthesis occurred by Hour 14. The timing of cell cycle progression that allowed escape from a dose of X irradiation that completely inhibited DNA synthesis was investigated. A growth-arrest point was identified at Hour 9 where 10 GY of X irradiation given before, but not after, completely inhibited earliest responding cells from entering DNA synthesis on schedule. Increased quantities of cells entered DNA synthesis on schedule as timing of the X irradiation was moved closer to the end of G1. Based on time relationships, the rise in protein synthesis is correlated with the sufficient event for the escape

In Vitro Effect of Lysozyme on Albumin Deposition to Hydrogel Contact Lens Materials.

Science.gov (United States)

Babaei Omali, Negar; Subbaraman, Lakshman N; Heynen, Miriam; Fadli, Zohra; Coles-Brennan, Chantal; Jones, Lyndon W

2017-11-01

Albumin deposition on contact lenses could be detrimental to contact lens (CL) wear because this may increase the risk of bacterial binding and reduce comfort. Lysozyme deposition on selected lens materials would reduce albumin deposition on lenses. This study aims to determine if lysozyme deposition on CLs could act as a barrier against subsequent albumin adsorption, using an in vitro model. Six hydrogel CL materials (etafilcon A, polymacon, nelfilcon A, omafilcon A, ocufilcon B, and nesofilcon A) were evaluated. Four CLs of each type were soaked in lysozyme solution for 16 hours at 37°C. Lysozyme-coated lenses were then placed in vials with 1.5 mL of artificial tear solution containing I-labeled albumin for 16 hours at 37°C with shaking. Four uncoated lenses of each type were used as controls. Lenses soaked in radiolabeled albumin were rinsed in a phosphate-buffered saline solution, and radioactive counts were measured directly on lenses using a gamma counter. Albumin uptake on lenses was measured using a calibration curve by plotting radioactive counts versus protein concentration. Results are reported as mean ± SD. Lysozyme-coated etafilcon A lenses exhibited lower levels of deposited albumin than uncoated etafilcon A lenses (58 ± 12 vs. 84 ± 5 ng/lens; P albumin adsorption between control (uncoated) and lysozyme-coated polymacon (105 ± 10 vs. 110 ± 34 ng/lens), nelfilcon A (51 ± 7 vs. 42 ± 20 ng/lens), omafilcon A (90 ± 20 vs. 80 ± 38 ng/lens), ocufilcon B (87 ± 20 vs. 115 ± 50 ng/lens), and nesofilcon A (170 ± 29 vs. 161 ± 10 ng/lens) lens materials (P > .05). Uncoated nesofilcon A lenses deposited the highest amount of albumin when compared with other uncoated lenses (P albumin, which may potentially be beneficial to CL wearers.

Straylight Measurements in Contact Lens Wear

NARCIS (Netherlands)

van der Meulen, Ivanka J. E.; Engelbrecht, Leonore A.; van Vliet, Johannes M. J.; Lapid-Gortzak, Ruth; Nieuwendaal, Carla P.; Mourits, Maarten P.; Schlingemann, Reinier O.; van den Berg, Thomas J. T. P.

2010-01-01

Purpose: (1) To quantify the effect of contact lens wear on straylight in rigid and soft contact lens wearers and (2) to relate findings to morphological changes and subjective complaints. Methods: Straylight was measured using the Oculus C-Quant during contact lens wear and after contact lens

Quadrupole magnetic lens

International Nuclear Information System (INIS)

Piskunov, V.A.

1981-01-01

The following connection of windings of electromagnet is suggested for simplification of the design of qUadrupole magnetic lens intended for use in radiotechnical and electron-optical devices. The mentioned windings are connected with each other by a bridge scheme and the variable resistors are switched in its diagonals in the lens containing four electromagnet with windings connected with two variable resistors the mobile contacts of which are connected with a direct current source. Current redistribution between left windings and right windings takes place at shift of mobile contact of variable resistor, and current redistribution between upper and low coils of electromagnets takes place at shifting mobile contact of the other variable resistor. In this case smooth and independent electron-optical misalignment of lens by two mutually perpendicular directions proceeds. Use of the given design of the lens in the oscillograph permits to use printing assembly for alignment plate and to reduce the number of connections at the expense of decreasing the number of resistors

Contact lens surface by electron beam

International Nuclear Information System (INIS)

Shin, Jung Hyuck; Lee, Suk Ju; Hwang, Kwang Ha; Jeon Jin

2011-01-01

Contact lens materials needs good biocompatibility, high refractive index, high optical transparency, high water content etc. Surface treat method by using plasma and radiation can modify the physical and/or chemical properties of the contact lens surface. Radiation technology such as electron beam irradiation can apply to polymerization reaction and enhance the functionality of the polymer.The purpose of this study is to modify of contact lens surface by using Eb irradiation technology. Electron beam was irradiated to the contact lens surface which was synthesized thermal polymerization method and commercial contact lens to modify physical and chemical properties. Ft-IR, XP, UV-vis spectrophotometer, water content, oxygen trans-metastability were used to characterize the surface state, physicochemical, and optical property of the contact lens treated with Eb. The water content and oxygen transmissibility of the contact lens treated with Eb were increased due to increase in the hydrophilic group such as O-C=O and OH group on the contact lens surface which could be produced by possible reaction between carbon and oxygen during the Eb irradiation. All of the lenses showed the high optical transmittance above 90%. In this case of B/Es, TES, Ti contact lens, the optical transmittance decreased about 5% with increasing Eb dose in the wavelength of UV-B region. The contact lens modified by Eb irradiation could improve the physical properties of the contact lens such as water content and oxygen transmissibility

Role of pirenoxine in the effects of catalin on in vitro ultraviolet-induced lens protein turbidity and selenite-induced cataractogenesis in vivo.

Science.gov (United States)

Hu, Chao-Chien; Liao, Jiahn-Haur; Hsu, Kuang-Yang; Lin, I-Lin; Tsai, Ming-Hsuan; Wu, Wen-Hsin; Wei, Tzu-Tang; Huang, Yi-Shiang; Chiu, Shih-Jiuan; Chen, Hsiang-Yin; Wu, Shih-Hsiung; Wu, Tzu-Hua

2011-01-01

In this study, we investigated the biochemical pharmacology of pirenoxine (PRX) and catalin under in vitro selenite/calcium- and ultraviolet (UV)-induced lens protein turbidity challenges. The systemic effects of catalin were determined using a selenite-induced cataractogenesis rat model. In vitro cataractogenesis assay systems (including UVB/C photo-oxidation of lens crystallins, calpain-induced proteolysis, and selenite/calcium-induced turbidity of lens crystallin solutions) were used to screen the activity of PRX and catalin eye drop solutions. Turbidity was identified as the optical density measured using spectroscopy at 405 nm. We also determined the in vivo effects of catalin on cataract severity in a selenite-induced cataract rat model. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was applied to analyze the integrity of crystallin samples. PRX at 1,000 μM significantly delayed UVC-induced turbidity formation compared to controls after 4 h of UVC exposure (pturbidity induced by 4 h of UVC exposure was ameliorated in the presence of catalin equivalent to 1~100 μM PRX in a concentration-dependent manner. Samples with catalin-formulated vehicle only (CataV) and those containing PRX equivalent to 100 μM had a similar protective effect after 4 h of UVC exposure compared to the controls (pturbidity formation compared to controls on days 0~4 (pturbidity on day 1 (pturbidity but required millimolar levels to protect against UVC irradiation. The observed inhibition of UVC-induced turbidity of lens crystallins by catalin at micromolar concentrations may have been a result of the catalin-formulated vehicle. Transient protection by catalin against selenite-induced turbidity of crystallin solutions in vitro was supported by the ameliorated cataract scores in the early stage of cataractogenesis in vivo by subcutaneously administered catalin. PRX could not inhibit calpain-induced proteolysis activated by calcium or catalin itself, and may be

Protein interfacial structure and nanotoxicology

Energy Technology Data Exchange (ETDEWEB)

White, John W. [Research School of Chemistry, Australian National University, Canberra (Australia)], E-mail: jww@rsc.anu.edu.au; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M. [Research School of Chemistry, Australian National University, Canberra (Australia)

2009-02-21

Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between {beta}-casein and {kappa}-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a {beta}-casein monolayer is attacked by a {kappa}-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a {beta}-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

Protein interfacial structure and nanotoxicology

International Nuclear Information System (INIS)

White, John W.; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M.

2009-01-01

Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between β-casein and κ-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a β-casein monolayer is attacked by a κ-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a β-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

PSAIA – Protein Structure and Interaction Analyzer

Directory of Open Access Journals (Sweden)

Vlahoviček Kristian

2008-04-01

Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

The structure of a cholesterol-trapping protein

Science.gov (United States)

cholesterol-trapping protein Contact: Dan Krotz, dakrotz@lbl.gov Berkeley Lab Science Beat Lab website index Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream. Knowing the structure of the protein, a cellular receptor that ensnares

Properties of the cathode lens combined with a focusing magnetic/immersion-magnetic lens

International Nuclear Information System (INIS)

Konvalina, I.; Muellerova, I.

2011-01-01

The cathode lens is an electron optical element in an emission electron microscope accelerating electrons from the sample, which serves as a source for a beam of electrons. Special application consists in using the cathode lens first for retardation of an illuminating electron beam and then for acceleration of reflected as well as secondary electrons, made in the directly imaging low energy electron microscope or in its scanning version discussed here. In order to form a real image, the cathode lens has to be combined with a focusing magnetic lens or a focusing immersion-magnetic lens, as used for objective lenses of some commercial scanning electron microscopes. These two alternatives are compared with regards to their optical properties, in particular with respect to predicted aberration coefficients and the spot size, as well as the optimum angular aperture of the primary beam. The important role of the final aperture size on the image resolution is also presented.

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

Science.gov (United States)

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

Function and structure of GFP-like proteins in the protein data bank.

Science.gov (United States)

Ong, Wayne J-H; Alvarez, Samuel; Leroux, Ivan E; Shahid, Ramza S; Samma, Alex A; Peshkepija, Paola; Morgan, Alicia L; Mulcahy, Shawn; Zimmer, Marc

2011-04-01

The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

Classification of proteins: available structural space for molecular modeling.

Science.gov (United States)

Andreeva, Antonina

2012-01-01

The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

Protein structural similarity search by Ramachandran codes

Directory of Open Access Journals (Sweden)

Chang Chih-Hung

2007-08-01

Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

Functional classification of protein structures by local structure matching in graph representation.

Science.gov (United States)

Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

2018-03-31

As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Intraocular lens fabrication

Energy Technology Data Exchange (ETDEWEB)

Salazar, M.A.; Foreman, L.R.

1997-07-08

This invention describes a method for fabricating an intraocular lens made from clear Teflon{trademark}, Mylar{trademark}, or other thermoplastic material having a thickness of about 0.025 millimeters. These plastic materials are thermoformable and biocompatable with the human eye. The two shaped lenses are bonded together with a variety of procedures which may include thermosetting and solvent based adhesives, laser and impulse welding, and ultrasonic bonding. The fill tube, which is used to inject a refractive filling material is formed with the lens so as not to damage the lens shape. A hypodermic tube may be included inside the fill tube. 13 figs.

Proteins with Novel Structure, Function and Dynamics

Science.gov (United States)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Selenite and ebselen supplementation attenuates D-galactose-induced oxidative stress and increases expression of SELR and SEP15 in rat lens.

Science.gov (United States)

Dai, Jie; Zhou, Jun; Liu, Hongmei; Huang, Kaixun

2016-12-01

Selenite and ebselen supplementation has been shown to possess anti-cataract potential in some experimental animal models of cataract, however, the underlying mechanisms remain unclear. The present study was designed to evaluate the anti-cataract effects and the underlying mechanisms of selenite and ebselen supplementation on galactose induced cataract in rats, a common animal model of sugar cataract. Transmission electron microscopy images of lens fiber cells (LFC) and lens epithelial cells (LEC) were observed in D-galactose-induced experimental cataractous rats treated with or without selenite and ebselen, also redox homeostasis and expression of proteins such as selenoprotein R (SELR), 15kD selenoprotein (SEP15), superoxide dismutase 1 (SOD1), catalase (CAT), β-crystallin protein, aldose reductase (AR) and glucose-regulated protein 78 (GRP78) were estimated in the lenses. The results showed that D-galactose injection injured rat lens and resulted in cataract formation; however, selenite and ebselen supplementation markedly alleviated ultrastructural injury of LFC and LEC. Moreover, selenite and ebselen supplementation could mitigate the oxidative damage in rat lens and increase the protein expressions of SELR, SEP15, SOD1, CAT and β-crystallin, as well as decrease the protein expressions of AR and GRP78. Taken together, these findings for the first time reveal the anti-cataract potential of selenite and ebselen in galactosemic cataract, and provide important new insights into the anti-cataract mechanisms of selenite and ebselen in sugar cataract.

Preliminary Investigation of an Active PLZT Lens

Science.gov (United States)

Lightsey, W. D.; Peters, B. R.; Reardon, P. J.; Wong, J. K.

2001-01-01

The design, analysis and preliminary testing of a prototype Adjustable Focus Optical Correction Lens (AFOCL) is described. The AFOCL is an active optical component composed of solid state lead lanthanum-modified zirconate titanate (PLZT) ferroelectric ceramic with patterned indium tin oxide (ITO) transparent surface electrodes that modulate the refractive index of the PLZT to function as an electro-optic lens. The AFOCL was developed to perform optical re-alignment and wavefront correction to enhance the performance of Ultra-Lightweight Structures and Space Observatories (ULSSO). The AFOCL has potential application as an active optical component within a larger optical system. As such, information from a wavefront sensor would be processed to provide input to the AFOCL to drive the sensed wavefront to the desired shape and location. While offering variable and rapid focussing capability (controlled wavefront manipulation) similar to liquid crystal based spatial light modulators (SLM), the AFOCL offers some potential advantages because it is a solid-state, stationary, low-mass, rugged, and thin optical element that can produce wavefront quality comparable to the solid refractive lens it replaces. The AFOCL acts as a positive or negative lens by producing a parabolic phase-shift in the PLZT material through the application of a controlled voltage potential across the ITO electrodes. To demonstrate the technology, a 4 mm diameter lens was fabricated to produce 5-waves of optical power operating at 2.051 micrometer wavelength. Optical metrology was performed on the device to measure focal length, optical quality, and efficiency for a variety of test configurations. The data was analyzed and compared to theoretical data available from computer-based models of the AFOCL.

21 CFR 886.1375 - Bagolini lens.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Bagolini lens. 886.1375 Section 886.1375 Food and... OPHTHALMIC DEVICES Diagnostic Devices § 886.1375 Bagolini lens. (a) Identification. A Bagolini lens is a device that consists of a plane lens containing almost imperceptible striations that do not obscure...

Structure and function of nanoparticle-protein conjugates

International Nuclear Information System (INIS)

Aubin-Tam, M-E; Hamad-Schifferli, K

2008-01-01

Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle-protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Site-specific labeling is desirable in order to control the protein orientation on the nanoparticle, which is crucial in many applications such as fluorescence resonance energy transfer. We evaluate methods for successful site-specific attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed. We also examine how molecular dynamics simulations of conjugates would complete those experimental techniques in order to provide atomistic details on the effect of nanoparticle attachment. Characterization studies of nanoparticle-protein complexes show that the structure and function are influenced by the chemistry of the nanoparticle ligand, the nanoparticle size, the nanoparticle material, the stoichiometry of the conjugates, the labeling site on the protein and the nature of the linkage (covalent versus non-covalent)

Experimental Analysis of Desalination Unit Coupled with Solar Water Lens Concentrator

Science.gov (United States)

Chaithanya, K. K.; Rajesh, V. R.; Suresh, Rahul

2016-09-01

The main problem that the world faces in this scenario is shortage of potable water. Hence this research work rivets to increase the yield of desalination system in an economical way. The integration of solar concentrator and desalination unit can project the desired yield, but the commercially available concentrated solar power technologies (CSP) are not economically viable. So this study proposes a novel method to concentrate ample amount of solar radiation in a cost effective way. Water acting as lens is a highlighted technology initiated in this work, which can be a substitute for CSP systems. And water lens can accelerate the desalination process so as to increase the yield economically. The solar irradiance passing through the water will be concentrated at a focal point, and the concentration depends on curvature of water lens. The experimental analysis of water lens makes use of transparent thin sheet, supported on a metallic structure. The Plano convex shape of water lens is developed by varying the volume of water that is being poured on the transparent thin sheet. From the experimental analysis it is inferred that, as the curvature of water lens increases, solar irradiance can be focused more accurately on to the focus and a higher water temperature is obtained inside the solar still.

Protein structure database search and evolutionary classification.

Science.gov (United States)

Yang, Jinn-Moon; Tung, Chi-Hua

2006-01-01

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

Modeling protein structures: construction and their applications.

Science.gov (United States)

Ring, C S; Cohen, F E

1993-06-01

Although no general solution to the protein folding problem exists, the three-dimensional structures of proteins are being successfully predicted when experimentally derived constraints are used in conjunction with heuristic methods. In the case of interleukin-4, mutagenesis data and CD spectroscopy were instrumental in the accurate assignment of secondary structure. In addition, the tertiary structure was highly constrained by six cysteines separated by many residues that formed three disulfide bridges. Although the correct structure was a member of a short list of plausible structures, the "best" structure was the topological enantiomer of the experimentally determined conformation. For many proteases, other experimentally derived structures can be used as templates to identify the secondary structure elements. In a procedure called modeling by homology, the structure of a known protein is used as a scaffold to predict the structure of another related protein. This method has been used to model a serine and a cysteine protease that are important in the schistosome and malarial life cycles, respectively. The model structures were then used to identify putative small molecule enzyme inhibitors computationally. Experiments confirm that some of these nonpeptidic compounds are active at concentrations of less than 10 microM.

An analytical method for predicting the geometrical and optical properties of the human lens under accommodation.

Science.gov (United States)

Sheil, Conor J; Bahrami, Mehdi; Goncharov, Alexander V

2014-05-01

We present an analytical method to describe the accommodative changes in the human crystalline lens. The method is based on the geometry-invariant lens model, in which the gradient-index (GRIN) iso-indicial contours are coupled to the external shape. This feature ensures that any given number of iso-indicial contours does not change with accommodation, which preserves the optical integrity of the GRIN structure. The coupling also enables us to define the GRIN structure if the radii and asphericities of the external lens surfaces are known. As an example, the accommodative changes in lenticular radii and central thickness were taken from the literature, while the asphericities of the external surfaces were derived analytically by adhering to the basic physical conditions of constant lens volume and its axial position. The resulting changes in lens geometry are consistent with experimental data, and the optical properties are in line with expected values for optical power and spherical aberration. The aim of the paper is to provide an anatomically and optically accurate lens model that is valid for 3 mm pupils and can be used as a new tool for better understanding of accommodation.

Improving the accuracy of protein secondary structure prediction using structural alignment

Directory of Open Access Journals (Sweden)

Gallin Warren J

2006-06-01

Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

Effect of gamma irradiation on in vitro bovine lens proteins

International Nuclear Information System (INIS)

Bernardes, D.M.L.; Mastro, N.L. del.

1988-07-01

The radiosensitivity of the ocular lens manifested by cataract formation has been of considerable interest in the study on the biological efects of radiations. Cataract can ben produced by different causes and also for the normal process of ageing. The aim of this work was to develop an in vitro system similar to in vivo cataract formation. It was used an aqueous solution of bovine lenses. The lenses after surgical removal mechanical and ultrasonic disrupted. The suspension was centrifuged and the supernatant was dialyzed and irradiated with different doses of 60 Co radiation. The opacification extent was measured in an spectrophotometer. (author) [pt

Lens epithelial cell apoptosis is an early event in the development of UVB-induced cataract.

Science.gov (United States)

Li, W C; Spector, A

1996-01-01

Epidemiological and experimental studies have revealed that exposure to UV can induce cataractogenesis. To investigate the mechanism of this induction, viability of the lens epithelial cells from UVB-treated rat lenses were examined. Irradiation of the cultured rat lenses with 8 J/s/m2 UVB for 60 min triggers lens epithelial cell apoptosis as determined by terminal deoxyribonucleotide transferase (TdT) labeling and DNA fragmentation assays. The apoptotic lens epithelial cells were initially found in the equatorial region and then quickly appeared in both equatorial and central regions. The percentage of apoptotic cells continuously increased during the postirradiation incubation. After a 5-h post-UVB incubation, more than 50% of the lens epithelial cells were apoptotic. By 24 h, all of the lens epithelial cells in the irradiated lenses were dead through apoptosis. Associated with this apoptotic process is a large upregulation of the proto-oncogene, c-fos. Opacification appears to follow the death of lens epithelial cells occurring first in the equatorial region and then in the central area. This is also true of classical cataract parameters such as non-protein thiol and wet weight, which are significantly modified only after appreciable epithelial cell apoptosis. Together, these results suggest that the rapid apoptotic death of the lens epithelial cells induced by UVB initiates cataract development.

A Tribute to Len Barton

Science.gov (United States)

Tomlinson, Sally

2010-01-01

This article constitutes a short personal tribute to Len Barton in honour of his work and our collegial relationship going back over 30 years. It covers how Len saw his intellectual project of providing critical sociological and political perspectives on special education, disability and inclusion, and his own radical political perspectives. Len's…

Exploring the universe of protein structures beyond the Protein Data Bank.

Science.gov (United States)

Cossio, Pilar; Trovato, Antonio; Pietrucci, Fabio; Seno, Flavio; Maritan, Amos; Laio, Alessandro

2010-11-04

It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. Beside their conceptual relevance, the new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the identification and design of novel folds.

Cross-linking of lens crystallin proteins induced by tryptophan metabolites and metal ions

DEFF Research Database (Denmark)

Tweeddale, Helen J; Hawkins, Clare Louise; Janmie, Joane F

2016-01-01

Long-wavelength solar UV radiation is implicated in photodamage to the human eye. The human lens contains multiple tryptophan-derived compounds that have significant absorbance bands in the UVA region (λ 315-400 nm) that act as efficient physical filters for these wavelengths. The concentrations...

THE BOSS EMISSION-LINE LENS SURVEY (BELLS). I. A LARGE SPECTROSCOPICALLY SELECTED SAMPLE OF LENS GALAXIES AT REDSHIFT {approx}0.5

Energy Technology Data Exchange (ETDEWEB)

Brownstein, Joel R.; Bolton, Adam S.; Pandey, Parul [Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112 (United States); Schlegel, David J. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Eisenstein, Daniel J. [Harvard College Observatory, 60 Garden Street, MS 20, Cambridge, MA 02138 (United States); Kochanek, Christopher S. [Department of Astronomy and Center for Cosmology and Astroparticle Physics, Ohio State University, Columbus, OH 43210 (United States); Connolly, Natalia [Department of Physics, Hamilton College, Clinton, NY 13323 (United States); Maraston, Claudia [Institute of Cosmology and Gravitation, University of Portsmouth, Portsmouth PO1 3FX (United Kingdom); Seitz, Stella [University Observatory Munich, Scheinstrasse 1, 81679 Muenchen (Germany); Wake, David A. [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Wood-Vasey, W. Michael [Pittsburgh Center for Particle Physics, Astrophysics, and Cosmology (PITT-PACC), Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260 (United States); Brinkmann, Jon [Apache Point Observatory, P.O. Box 59, Sunspot, NM 88349 (United States); Schneider, Donald P. [Department of Astronomy and Astrophysics and Institute for Gravitation and the Cosmos, Pennsylvania State University, University Park, PA 16802 (United States); Weaver, Benjamin A. [Center for Cosmology and Particle Physics, New York University, New York, NY 10003 (United States)

2012-01-01

We present a catalog of 25 definite and 11 probable strong galaxy-galaxy gravitational lens systems with lens redshifts 0.4 {approx}< z {approx}< 0.7, discovered spectroscopically by the presence of higher-redshift emission lines within the Baryon Oscillation Spectroscopic Survey (BOSS) of luminous galaxies, and confirmed with high-resolution Hubble Space Telescope (HST) images of 44 candidates. Our survey extends the methodology of the Sloan Lens Advanced Camera for Surveys survey (SLACS) to higher redshift. We describe the details of the BOSS spectroscopic candidate detections, our HST ACS image processing and analysis methods, and our strong gravitational lens modeling procedure. We report BOSS spectroscopic parameters and ACS photometric parameters for all candidates, and mass-distribution parameters for the best-fit singular isothermal ellipsoid models of definite lenses. Our sample to date was selected using only the first six months of BOSS survey-quality spectroscopic data. The full five-year BOSS database should produce a sample of several hundred strong galaxy-galaxy lenses and in combination with SLACS lenses at lower redshift, strongly constrain the redshift evolution of the structure of elliptical, bulge-dominated galaxies as a function of luminosity, stellar mass, and rest-frame color, thereby providing a powerful test for competing theories of galaxy formation and evolution.

Stop grating for perfect replication of micro Fresnel lens by thermal imprinting

International Nuclear Information System (INIS)

Gao, Yulong; Lin, Jie; Jin, Peng; Tan, Jiubin; Davies, Graham; Prewett, Philip D

2012-01-01

A stop grating concept is proposed to improve polymer filling in the thermal imprinting of a micro Fresnel lens structure. The stop grating consists of line and space structures outside the Fresnel lens pattern zone area. The experimental results have proved that the stop grating can help to achieve the complete filling of a mold, at the same time acting as a stop to prevent possible damage to the mold surface relief structures during imprinting press. A computer simulation was carried out to identify the phenomena of micro-holes at the edge of imprinted pattern. By removing the cavity between the pattern area and stop grating, perfect imprinting results have been achieved. (paper)

Solution NMR structure determination of proteins revisited

International Nuclear Information System (INIS)

Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

2008-01-01

This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

K-nearest uphill clustering in the protein structure space

KAUST Repository

Cui, Xuefeng; Gao, Xin

2016-01-01

The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated

Binding free energy analysis of protein-protein docking model structures by evERdock.

Science.gov (United States)

Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

2018-03-14

To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

The Master Lens Database and The Orphan Lenses Project

Science.gov (United States)

Moustakas, Leonidas

2012-10-01

Strong gravitational lenses are uniquely suited for the study of dark matter structure and substructure within massive halos of many scales, act as gravitational telescopes for distant faint objects, and can give powerful and competitive cosmological constraints. While hundreds of strong lenses are known to date, spanning five orders of magnitude in mass scale, thousands will be identified this decade. To fully exploit the power of these objects presently, and in the near future, we are creating the Master Lens Database. This is a clearinghouse of all known strong lens systems, with a sophisticated and modern database of uniformly measured and derived observational and lens-model derived quantities, using archival Hubble data across several instruments. This Database enables new science that can be done with a comprehensive sample of strong lenses. The operational goal of this proposal is to develop the process and the code to semi-automatically stage Hubble data of each system, create appropriate masks of the lensing objects and lensing features, and derive gravitational lens models, to provide a uniform and fairly comprehensive information set that is ingested into the Database. The scientific goal for this team is to use the properties of the ensemble of lenses to make a new study of the internal structure of lensing galaxies, and to identify new objects that show evidence of strong substructure lensing, for follow-up study. All data, scripts, masks, model setup files, and derived parameters, will be public, and free. The Database will be accessible online and through a sophisticated smartphone application, which will also be free.

A course in lens design

CERN Document Server

Velzel, Chris

2014-01-01

A Course in Lens Design is an instruction in the design of image-forming optical systems. It teaches how a satisfactory design can be obtained in a straightforward way. Theory is limited to a minimum, and used to support the practical design work. The book introduces geometrical optics, optical instruments and aberrations. It gives a description of the process of lens design and of the strategies used in this process. Half of its content is devoted to the design of sixteen types of lenses, described in detail from beginning to end. This book is different from most other books on lens design because it stresses the importance of the initial phases of the design process: (paraxial) lay-out and (thin-lens) pre-design. The argument for this change of accent is that in these phases much information can be obtained about the properties of the lens to be designed. This information can be used in later phases of the design. This makes A Course in Lens Design a useful self-study book, and a suitable basis for an intro...

Development of Fresnel lens for improvement of rear visibility; Shikai kojo Fresnel lens no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

Iwamoto, K; Sanada, C; Tsukino, M [Nissan Motor Co. Ltd., Tokyo (Japan)

1997-10-01

Fresnel lenses have been widely used to increase the visual field around vehicles for drivers. However, internal reflection in these lenses has been an obstacle in producing dear images. This internal glow is generated by incident light from an unexpected direction reflecting on the non-lens surface or radiating from the non-lens surface of the Fresnel lens. The cause of internal glow has been made dear combining louver film with the lens. The newly developed technology removes obstacles in producing dear images by reducing internal glow. 7 figs.

Curiosity's Mars Hand Lens Imager (MAHLI): Inital Observations and Activities

Science.gov (United States)

Edgett, K. S.; Yingst, R. A.; Minitti, M. E.; Robinson, M. L.; Kennedy, M. R.; Lipkaman, L. J.; Jensen, E. H.; Anderson, R. C.; Bean, K. M.; Beegle, L. W.;

Vitrectorhexis and lens aspiration with posterior chamber intraocular lens implantation in spherophakia.

Science.gov (United States)

Al-Haddad, Christiane; Khatib, Lama

2012-07-01

We describe a technique that uses the vitrector to perform successful lens aspiration and posterior chamber intraocular lens (IOL) implantation in children with spherophakia and anterior lens subluxation. After an anterior chamber maintainer is placed, the ocutome is introduced through a limbal incision to perform a circular vitrectorhexis to avoid excessive manipulation of the unstable lens followed by gentle cortex aspiration. A foldable IOL is injected into the sulcus (3-piece IOL) or bag (1-piece IOL) if the capsule is sufficiently stable. Through a pars plana incision, the ocutome is then used to perform a posterior capsulotomy to prevent late posterior capsule opacification. In our patient, sulcus IOL placement was more stable than in-the-bag placement. Neither author has a financial or proprietary interest in any material or method mentioned. Copyright © 2012 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Pentacam Scheimpflug quantitative imaging of the crystalline lens and intraocular lens.

Science.gov (United States)

Rosales, Patricia; Marcos, Susana

2009-05-01

To implement geometrical and optical distortion correction methods for anterior segment Scheimpflug images obtained with a commercially available system (Pentacam, Oculus Optikgeräte GmbH). Ray tracing algorithms were implemented to obtain corrected ocular surface geometry from the original images captured by the Pentacam's CCD camera. As details of the optical layout were not fully provided by the manufacturer, an iterative procedure (based on imaging of calibrated spheres) was developed to estimate the camera lens specifications. The correction procedure was tested on Scheimpflug images of a physical water cell model eye (with polymethylmethacrylate cornea and a commercial IOL of known dimensions) and of a normal human eye previously measured with a corrected optical and geometrical distortion Scheimpflug camera (Topcon SL-45 [Topcon Medical Systems Inc] from the Vrije University, Amsterdam, Holland). Uncorrected Scheimpflug images show flatter surfaces and thinner lenses than in reality. The application of geometrical and optical distortion correction algorithms improves the accuracy of the estimated anterior lens radii of curvature by 30% to 40% and of the estimated posterior lens by 50% to 100%. The average error in the retrieved radii was 0.37 and 0.46 mm for the anterior and posterior lens radii of curvature, respectively, and 0.048 mm for lens thickness. The Pentacam Scheimpflug system can be used to obtain quantitative information on the geometry of the crystalline lens, provided that geometrical and optical distortion correction algorithms are applied, within the accuracy of state-of-the art phakometry and biometry. The techniques could improve with exact knowledge of the technical specifications of the instrument, improved edge detection algorithms, consideration of aspheric and non-rotationally symmetrical surfaces, and introduction of a crystalline gradient index.

Luneburg lens in silicon photonics.

Science.gov (United States)

Di Falco, Andrea; Kehr, Susanne C; Leonhardt, Ulf

2011-03-14

The Luneburg lens is an aberration-free lens that focuses light from all directions equally well. We fabricated and tested a Luneburg lens in silicon photonics. Such fully-integrated lenses may become the building blocks of compact Fourier optics on chips. Furthermore, our fabrication technique is sufficiently versatile for making perfect imaging devices on silicon platforms.

Resistance of Pseudomonas aeruginosa isolates to hydrogel contact lens disinfection correlates with cytotoxic activity.

Science.gov (United States)

Lakkis, C; Fleiszig, S M

2001-04-01

One of the most common pathogens in infection of hydrogel contact lens wearers is Pseudomonas aeruginosa, which can gain access to the eye via contamination of the lens, lens case, and lens care solutions. Only one strain per species is used in current regulatory testing for the marketing of chemical contact lens disinfectants. The aim of this study was to determine whether P. aeruginosa strains vary in their susceptibility to hydrogel contact lens disinfectants. A method for rapidly screening bacterial susceptibility to contact lens disinfectants was developed, based on measurement of the MIC. The susceptibility of 35 P. aeruginosa isolates to two chemical disinfectants was found to vary among strains. MICs ranged from 6.25 to 100% for both disinfectants at 37 degrees C, and a number of strains were not inhibited by a 100% disinfectant concentration in the lens case environment at room temperature (22 degrees C). Resistance to disinfection appeared to be an inherent rather than acquired trait, since some resistant strains had been isolated prior to the introduction of the disinfectants and some susceptible P. aeruginosa strains could not be made more resistant by repeated disinfectant exposure. A number of P. aeruginosa strains which were comparatively more resistant to short-term disinfectant exposure also demonstrated the ability to grow to levels above the initial inoculum in one chemical disinfectant after long-term (24 to 48 h) disinfectant exposure. Resistance was correlated with acute cytotoxic activity toward corneal epithelial cells and with exsA, which encodes a protein that regulates cytotoxicity via a complex type III secretion system. These results suggest that chemical disinfection solutions may select for contamination with cytotoxic strains. Further investigation of the mechanisms and factors responsible for resistance may also lead to strategies for reducing adverse responses to contact lens wear.

Integral membrane protein structure determination using pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

2015-04-15

Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

The Protein Model Portal--a comprehensive resource for protein structure and model information.

Science.gov (United States)

Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

2013-01-01

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org.

The Protein Model Portal—a comprehensive resource for protein structure and model information

Science.gov (United States)

Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

2013-01-01

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org PMID:23624946

Modern lens antennas for communications engineering

CERN Document Server

Thornton, John

2012-01-01

The aim of this book is to present the modern design principles and analysis of lens antennas. It gives graduates and RF/Microwave professionals the design insights in order to make full use of lens antennas.  Why do we want to write a book in lens antennas? Because this topic has not been thoroughly publicized, its importance is underestimated. As antennas play a key role in communication systems, recent development in wireless communications would indeed benefit from the characteristics of lens antennas: low profile, and low cost etc.  The major advantages of lens antennas are na

Dynamics of focused femtosecond laser pulse during photodisruption of crystalline lens

Science.gov (United States)

Gupta, Pradeep Kumar; Singh, Ram Kishor; Sharma, R. P.

2018-04-01

Propagation of laser pulses of femtosecond time duration (focused through a focusing lens inside the crystalline lens) has been investigated in this paper. Transverse beam diffraction, group velocity dispersion, graded refractive index structure of the crystalline lens, self-focusing, and photodisruption in which plasma is formed due to the high intensity of laser pulses through multiphoton ionization have been taken into account. The model equations are the modified nonlinear Schrödinger equation along with a rate equation that takes care of plasma generation. A close analysis of model equations suggests that the femtosecond laser pulse duration is critical to the breakdown in the lens. Our numerical simulations reveal that the combined effect of self-focusing and multiphoton ionization provides the breakdown threshold. During the focusing of femtosecond laser pulses, additional spatial pulse splitting arises along with temporal splitting. This splitting of laser pulses arises on account of self-focusing, laser induced breakdown, and group velocity distribution, which modifies the shape of laser pulses. The importance of the present study in cavitation bubble generation to improve the elasticity of the eye lens has also been discussed in this paper.

Changes in monkey crystalline lens spherical aberration during simulated accommodation in a lens stretcher.

Science.gov (United States)

Maceo Heilman, Bianca; Manns, Fabrice; de Castro, Alberto; Durkee, Heather; Arrieta, Esdras; Marcos, Susana; Parel, Jean-Marie

2015-02-10

The purpose of this study was to quantify accommodation-induced changes in the spherical aberration of cynomolgus monkey lenses. Twenty-four lenses from 20 cynomolgus monkeys (Macaca fascicularis; 4.4-16.0 years of age; postmortem time 13.5 ± 13.0 hours) were mounted in a lens stretcher. Lens spherical aberration was measured in the unstretched (accommodated) and stretched (relaxed) states with a laser ray tracing system that delivered 51 equally spaced parallel rays along 1 meridian of the lens over the central 6-mm optical zone. A camera mounted below the lens was used to measure the ray height at multiple positions along the optical axis. For each entrance ray, the change in ray height with axial position was fitted with a third-order polynomial. The effective paraxial focal length and Zernike spherical aberration coefficients corresponding to a 6-mm pupil diameter were extracted from the fitted values. The unstretched lens power decreased with age from 59.3 ± 4.0 diopters (D) for young lenses to 45.7 ± 3.1 D for older lenses. The unstretched lens shifted toward less negative spherical aberration with age, from -6.3 ± 0.7 μm for young lenses to -5.0 ± 0.5 μm for older lenses. The power and spherical aberration of lenses in the stretched state were independent of age, with values of 33.5 ± 3.4 D and -2.6 ± 0.5 μm, respectively. Spherical aberration is negative in cynomolgus monkey lenses and becomes more negative with accommodation. These results are in good agreement with the predicted values using computational ray tracing in a lens model with a reconstructed gradient refractive index. The spherical aberration of the unstretched lens becomes less negative with age. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

Sampling Realistic Protein Conformations Using Local Structural Bias

DEFF Research Database (Denmark)

Hamelryck, Thomas Wim; Kent, John T.; Krogh, A.

2006-01-01

The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which...... are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded...... in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications...

A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

Science.gov (United States)

Fan, Ming; Zheng, Bin; Li, Lihua

2015-10-01

Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request.

Fabrication of polycrystalline diamond refractive X-ray lens by femtosecond laser processing

Energy Technology Data Exchange (ETDEWEB)

Kononenko, T.V.; Ralchenko, V.G.; Ashkinazi, E.E.; Konov, V.I. [General Physics Institute of Russian Academy of Sciences, Moscow (Russian Federation); National Research Nuclear University ' ' MEPhI' ' , Moscow (Russian Federation); Polikarpov, M.; Ershov, P. [Immanuel Kant Baltic Federal University, Functional Nanomaterials, Kaliningrad (Russian Federation); Kuznetsov, S.; Yunkin, V. [Institute of Microelectronics Technology RAS, Chernogolovka, Moscow region (Russian Federation); Snigireva, I. [European Synchrotron Radiation Facility, Grenoble (France)

2016-03-15

X-ray planar compound refractive lenses were fabricated from a polycrystalline diamond plate grown by chemical vapor deposition, by precise through cutting with femtosecond laser pulses. The lens geometry and the surface morphology were investigated with optical and scanning electron microscopy, while the material structure modification was analyzed by Raman spectroscopy. The results of the preliminary lens test at 9.25-keV X-rays are presented. (orig.)

Fabrication of polycrystalline diamond refractive X-ray lens by femtosecond laser processing

International Nuclear Information System (INIS)

Kononenko, T.V.; Ralchenko, V.G.; Ashkinazi, E.E.; Konov, V.I.; Polikarpov, M.; Ershov, P.; Kuznetsov, S.; Yunkin, V.; Snigireva, I.

2016-01-01

X-ray planar compound refractive lenses were fabricated from a polycrystalline diamond plate grown by chemical vapor deposition, by precise through cutting with femtosecond laser pulses. The lens geometry and the surface morphology were investigated with optical and scanning electron microscopy, while the material structure modification was analyzed by Raman spectroscopy. The results of the preliminary lens test at 9.25-keV X-rays are presented. (orig.)

Symmetric lens with extended depth of focus

OpenAIRE

Cho, Sung Nae

2008-01-01

The lens surface profile is derived based on the instantaneous focal length versus the lens radius data. The lens design based on instantaneous focal length versus the lens radius data has many useful applications in software assisted image focusing technology.

Accurate protein structure modeling using sparse NMR data and homologous structure information.

Science.gov (United States)

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Exploring the universe of protein structures beyond the Protein Data Bank.

Directory of Open Access Journals (Sweden)

Pilar Cossio

Full Text Available It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. Beside their conceptual relevance, the new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the identification and design of novel folds.

[Congenital lens subluxation: visual acuity outcomes and intraocular lens postoperative position].

Science.gov (United States)

Arraes, Caroline; Endriss, Daniela; Lobato, Francisco; Arraes, João; Ventura, Marcelo

2010-01-01

To evaluate the visual acuity outcomes and to investigate the intraocular lens (IOL) and endocapsular ring positions with ultrasound biomicroscopy in 17 eyes of 10 patients with congenital lens subluxation who underwent the same surgical technique, by the same surgeon. The study was performed in the ''Hospital de Olhos de Pernambuco'' and ''Fundação Altino Ventura''. The surgical technique consisted of phacoaspiration with implant of endocapsular ring and intraocular lens with one loop haptic amputated. The age varied from 7 to 22 years. Data on visual acuity (VA) before and after surgery, surgery follow-up period, and complications were analyzed. All patients underwent ultrasound biomicroscopy. The mean follow-up period was 2.8 years. There was a VA improvement in 17 (100%) eyes: in 12 eyes (70.6%) the visual acuity was better than 20/40; 4 (23.5%) ranged from 20/40 to 20/100, and 1 (5.9%) had visual acuity worse than 20/100, however better than the preoperative visual acuity. The posterior capsular opacification occurred in 10 eyes (58.9%). Ultrasound biomicroscopy showed that all IOL were partially decentralized, however without surpassing the pupil border limit. Endocapsular ring position was correct and there was a good capsular support in all cases. The evaluated surgical treatment provided good intraocular lens and endocapsular ring position, with VA improvement Thus, this technique is a viable, effective and safe option for the visual rehabilitation of patients with congenital lens subluxation.

Simultaneous determination of protein structure and dynamics

DEFF Research Database (Denmark)

Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

2005-01-01

at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

Compare local pocket and global protein structure models by small structure patterns

KAUST Repository

Cui, Xuefeng

2015-09-09

Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

The influence of end of day silicone hydrogel daily disposable contact lens fit on ocular comfort, physiology and lens wettability.

Science.gov (United States)

Wolffsohn, James; Hall, Lee; Mroczkowska, Stephanie; Hunt, Olivia A; Bilkhu, Paramdeep; Drew, Tom; Sheppard, Amy

2015-10-01

To quantify the end-of-day silicone-hydrogel daily disposable contact lens fit and its influence of on ocular comfort, physiology and lens wettability. Thirty-nine subjects (22.1±3.5 years) were randomised to wear each of 3 silicone-hydrogel daily-disposable contact lenses (narafilcon A, delefilcon A and filcon II 3), bilaterally, for one week. Lens fit was assessed objectively using a digital video slit-lamp at 8, 12 and 16h after lens insertion. Hyperaemia, non-invasive tear break-up time, tear meniscus height and comfort were also evaluated at these timepoints, while corneal and conjunctival staining were assessed on lens removal. Lens fit assessments were not different between brands (P>0.05), with the exception of the movement at blink where narafilcon A was more mobile. Overall, lag reduced but push-up speed increased from 8 to 12h (P0.05). Movement-on-blink was unaffected by wear-time (F=0.403, P=0.670). A more mobile lens fit with one brand did not indicate that person would have a more mobile fit with another brand (r=-0.06 to 0.63). Lens fit was not correlated with comfort, ocular physiology or lens wettability (P>0.01). Among the lenses tested, objective lens fit changed between 8h and 12h of lens wear. The weak correlation in individual lens fit between brands indicates that fit is dependent on more than ocular shape. Consequently, substitution of a different lens brand with similar parameters will not necessarily provide comparable lens fit. Copyright © 2015 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Hidden Structural Codes in Protein Intrinsic Disorder.

Science.gov (United States)

Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

2017-10-17

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

K-nearest uphill clustering in the protein structure space

KAUST Repository

Cui, Xuefeng

2016-08-26

The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated protein structure classifications (e.g., SCOP and CATH) are very successful, but recently suffer the slow updating problem because of the increased throughput of newly solved protein structures. Thus, fully automatic methods to cluster proteins in the protein structure space have been designed and developed. In this study, we observed that the SCOP superfamilies are highly consistent with clustering trees representing hierarchical clustering procedures, but the tree cutting is very challenging and becomes the bottleneck of clustering accuracy. To overcome this challenge, we proposed a novel density-based K-nearest uphill clustering method that effectively eliminates noisy pairwise protein structure similarities and identifies density peaks as cluster centers. Specifically, the density peaks are identified based on K-nearest uphills (i.e., proteins with higher densities) and K-nearest neighbors. To our knowledge, this is the first attempt to apply and develop density-based clustering methods in the protein structure space. Our results show that our density-based clustering method outperforms the state-of-the-art clustering methods previously applied to the problem. Moreover, we observed that computational methods and human experts could produce highly similar clusters at high precision values, while computational methods also suggest to split some large superfamilies into smaller clusters. © 2016 Elsevier B.V.

Visualization of transverse diffusion paths across fiber cells of the ocular lens by small animal MRI

International Nuclear Information System (INIS)

Vaghefi, Ehsan; Hunter, Peter J; Jacobs, Marc D; Pontre, Beau; Donaldson, Paul J

2009-01-01

The sense of vision requires that light penetrate through the ocular lens. Experiments, performed and published by many research groups, have suggested that the lens, which has no blood vessels, relies on internally directed ion and water fluxes for its circulation, survival and transparency. We investigated the internal diffusive pathways of the lens in order to better understand the constraints that may be operating on directional lens fluxes. Small animal magnetic resonance imaging, including T2-weighted and diffusion tensor imaging, was used to measure tissue properties and diffusivity throughout cultured bovine lenses. A range of concentric regions of signal intensity was distinguished inside the lens, by both T2-weighted signal and mean diffusivity. Diffusivity mapping of the lens revealed novel anisotropic polar and equatorial zones of pronounced diffusivity directed transverse to the fiber cells. In contrast, an inner zone including the lens nucleus showed isotropic and weak diffusivity. Our results lend support to models of internally directed lens micro-circulation, by placing non-structural diffusive constraints on global patterns of fluid circulation

Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

OpenAIRE

Wang, Liwen; Chance, Mark R.

2011-01-01

Structural MS is a rapidly growing field with many applications in basic research and pharmaceutical drug development. In this feature article the overall technology is described and several examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate protein structure, and identify ligand dependent conformational changes in proteins are described.

Extracting knowledge from protein structure geometry

DEFF Research Database (Denmark)

Røgen, Peter; Koehl, Patrice

2013-01-01

potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins...

Pseudomonas aeruginosa Infectious Keratitis in a High Oxygen Transmissible Rigid Contact Lens Rabbit Model

Science.gov (United States)

Wei, Cynthia; Zhu, Meifang; Petroll, W. Matthew; Robertson, Danielle M.

2014-01-01

Purpose. To establish a rabbit model of infectious Pseudomonas aeruginosa keratitis using ultrahigh oxygen transmissible rigid lenses and characterize the frequency and severity of infection when compared to a non–oxygen transmissible lens material. Methods. Rabbits were fit with rigid lenses composed of ultrahigh and non–oxygen transmissible materials. Prior to wear, lenses were inoculated with an invasive corneal isolate of P. aeruginosa stably conjugated to green fluorescent protein (GFP). Corneas were examined before and after lens wear using a modified Heidelberg Rostock Tomograph in vivo confocal microscope. Viable bacteria adherent to unworn and worn lenses were assessed by standard plate counts. The presence of P. aeruginosa-GFP and myeloperoxidase-labeled neutrophils in infected corneal tissue was evaluated using laser scanning confocal microscopy. Results. The frequency and severity of infectious keratitis was significantly greater with inoculated ultrahigh oxygen transmissible lenses. Infection severity was associated with increasing neutrophil infiltration and in severe cases, corneal melting. In vivo confocal microscopic analysis of control corneas following lens wear confirmed that hypoxic lens wear was associated with mechanical surface damage, whereas no ocular surface damage was evident in the high-oxygen lens group. Conclusions. These data indicate that in the absence of adequate tear clearance, the presence of P. aeruginosa trapped under the lens overrides the protective effects of oxygen on surface epithelial cells. These findings also suggest that alternative pathophysiological mechanisms exist whereby changes under the lens in the absence of frank hypoxic damage result in P. aeruginosa infection in the otherwise healthy corneal epithelium. PMID:25125601

Relationship between Molecular Structure Characteristics of Feed Proteins and Protein Digestibility and Solubility

Directory of Open Access Journals (Sweden)

Mingmei Bai

2016-08-01

Full Text Available The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003; moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004. On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001 and solubility (p = 0.002. These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

UV-blocking spectacle lens protects against UV-induced decline of visual performance.

Science.gov (United States)

Liou, Jyh-Cheng; Teng, Mei-Ching; Tsai, Yun-Shan; Lin, En-Chieh; Chen, Bo-Yie

2015-01-01

Excessive exposure to sunlight may be a risk factor for ocular diseases and reduced visual performance. This study was designed to examine the ability of an ultraviolet (UV)-blocking spectacle lens to prevent visual acuity decline and ocular surface disorders in a mouse model of UVB-induced photokeratitis. Mice were divided into 4 groups (10 mice per group): (1) a blank control group (no exposure to UV radiation), (2) a UVB/no lens group (mice exposed to UVB rays, but without lens protection), (3) a UVB/UV400 group (mice exposed to UVB rays and protected using the CR-39™ spectacle lens [UV400 coating]), and (4) a UVB/photochromic group (mice exposed to UVB rays and protected using the CR-39™ spectacle lens [photochromic coating]). We investigated UVB-induced changes in visual acuity and in corneal smoothness, opacity, and lissamine green staining. We also evaluated the correlation between visual acuity decline and changes to the corneal surface parameters. Tissue sections were prepared and stained immunohistochemically to evaluate the structural integrity of the cornea and conjunctiva. In blank controls, the cornea remained undamaged, whereas in UVB-exposed mice, the corneal surface was disrupted; this disruption significantly correlated with a concomitant decline in visual acuity. Both the UVB/UV400 and UVB/photochromic groups had sharper visual acuity and a healthier corneal surface than the UVB/no lens group. Eyes in both protected groups also showed better corneal and conjunctival structural integrity than unprotected eyes. Furthermore, there were fewer apoptotic cells and less polymorphonuclear leukocyte infiltration in corneas protected by the spectacle lenses. The model established herein reliably determines the protective effect of UV-blocking ophthalmic biomaterials, because the in vivo protection against UV-induced ocular damage and visual acuity decline was easily defined.

Polymer dispensing and embossing technology for the lens type LED packaging

Science.gov (United States)

Chien, Chien-Lin Chang; Huang, Yu-Che; Hu, Syue-Fong; Chang, Chung-Min; Yip, Ming-Chuen; Fang, Weileun

2013-06-01

This study presents a ring-type micro-structure design on the substrate and its corresponding micro fabrication processes for a lens-type light-emitting diode (LED) package. The dome-type or crater-type silicone lenses are achieved by a dispensing and embossing process rather than a molding process. Silicone with a high viscosity and thixotropy index is used as the encapsulant material. The ring-type micro structure is adopted to confine the dispensed silicone encapsulant so as to form the packaged lens. With the architecture and process described, this LED package technology herein has three merits: (1) the flexibility of lens-type LED package designs is enhanced; (2) a dome-type package design is used to enhance the intensity; (3) a crater-type package design is used to enhance the view angle. Measurement results show the ratio between the lens height and lens radius can vary from 0.4 to 1 by changing the volume of dispensed silicone. The view angles of dome-type and crater-type packages can reach 155° ± 5° and 175° ± 5°, respectively. As compared with the commercial plastic leaded chip carrier-type package, the luminous flux of a monochromatic blue light LED is improved by 15% by the dome-type package (improved by 7% by the crater-type package) and the luminous flux of a white light LED is improved by 25% by the dome-type package (improved by 13% by the crater-type package). The luminous flux of monochromatic blue light LED and white light LED are respectively improved by 8% and 12% by the dome-type package as compare with the crater-type package.

Automated protein structure calculation from NMR data

International Nuclear Information System (INIS)

Williamson, Mike P.; Craven, C. Jeremy

2009-01-01

Current software is almost at the stage to permit completely automatic structure determination of small proteins of <15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia

Process qualification and testing of LENS deposited AY1E0125 D-bottle brackets

International Nuclear Information System (INIS)

Atwood, Clinton J.; Smugeresky, John E.; Jew, Michael; Gill, David Dennis; Scheffel, Simon

2006-01-01

The LENS Qualification team had the goal of performing a process qualification for the Laser Engineered Net Shaping(trademark)(LENS(reg s ign)) process. Process Qualification requires that a part be selected for process demonstration. The AY1E0125 D-Bottle Bracket from the W80-3 was selected for this work. The repeatability of the LENS process was baselined to determine process parameters. Six D-Bottle brackets were deposited using LENS, machined to final dimensions, and tested in comparison to conventionally processed brackets. The tests, taken from ES1E0003, included a mass analysis and structural dynamic testing including free-free and assembly-level modal tests, and Haversine shock tests. The LENS brackets performed with very similar characteristics to the conventionally processed brackets. Based on the results of the testing, it was concluded that the performance of the brackets made them eligible for parallel path testing in subsystem level tests. The testing results and process rigor qualified the LENS process as detailed in EER200638525A

GRAVITATIONAL LENS MODELING WITH GENETIC ALGORITHMS AND PARTICLE SWARM OPTIMIZERS

International Nuclear Information System (INIS)

Rogers, Adam; Fiege, Jason D.

2011-01-01

Strong gravitational lensing of an extended object is described by a mapping from source to image coordinates that is nonlinear and cannot generally be inverted analytically. Determining the structure of the source intensity distribution also requires a description of the blurring effect due to a point-spread function. This initial study uses an iterative gravitational lens modeling scheme based on the semilinear method to determine the linear parameters (source intensity profile) of a strongly lensed system. Our 'matrix-free' approach avoids construction of the lens and blurring operators while retaining the least-squares formulation of the problem. The parameters of an analytical lens model are found through nonlinear optimization by an advanced genetic algorithm (GA) and particle swarm optimizer (PSO). These global optimization routines are designed to explore the parameter space thoroughly, mapping model degeneracies in detail. We develop a novel method that determines the L-curve for each solution automatically, which represents the trade-off between the image χ 2 and regularization effects, and allows an estimate of the optimally regularized solution for each lens parameter set. In the final step of the optimization procedure, the lens model with the lowest χ 2 is used while the global optimizer solves for the source intensity distribution directly. This allows us to accurately determine the number of degrees of freedom in the problem to facilitate comparison between lens models and enforce positivity on the source profile. In practice, we find that the GA conducts a more thorough search of the parameter space than the PSO.

Relation between native ensembles and experimental structures of proteins

DEFF Research Database (Denmark)

Best, R. B.; Lindorff-Larsen, Kresten; DePristo, M. A.

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of "high-sequence similarity Protein Data Bank" (HSP) structures and consider the extent to which such ensembles represent the structural...... Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest...... heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein...

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

Science.gov (United States)

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

A novel phosphorylcholine-coated contact lens for extended wear use.

Science.gov (United States)

Court, J L; Redman, R P; Wang, J H; Leppard, S W; Obyrne, V J; Small, S A; Lewis, A L; Jones, S A; Stratford, P W

2001-12-01

The preparation and characterisation of a new phosphorylcholine (PC)-coated silicone hydrogel contact lens for use in extended wear is described. The Michael-type addition of amines to acrylates forms the basis of the synthesis of a novel silicone-based macromer with hydrophilic functionality. It is demonstrated that this macromer can be combined with other silicone-based monomers, hydrophilic monomers and crosslinker to produce a contact lenses formulation. Examples of lenses with water contents of 33% and 46% are illustrated and their properties compared to other commercially available lenses. Materials with comparatively low modulus (2-4MPa) with excellent elongation to break (>200%) can be obtained using this technology. In addition to the mechanical aspects. both the oxygen and solute permeabilities of the material can be controlled by the hydrophilic: hydrophobic monomer balance in the formulation. to obtain materials with attributes suitable for extended wear use. The PC coating is achieved by means of an in-mould coating (IMC) technique that produces a uniform and stable surface as determined by staining and XPS. The coating imparts both improved lens wettability (advancing contact angle of approximately 50 with virtually no hysteresis) and lower protein adsorption relative to the uncoated lens.

Hydroimidazolone modification of the conserved Arg12 in small heat shock proteins: studies on the structure and chaperone function using mutant mimics.

Directory of Open Access Journals (Sweden)

Ram H Nagaraj

Full Text Available Methylglyoxal (MGO is an α-dicarbonyl compound present ubiquitously in the human body. MGO reacts with arginine residues in proteins and forms adducts such as hydroimidazolone and argpyrimidine in vivo. Previously, we showed that MGO-mediated modification of αA-crystallin increased its chaperone function. We identified MGO-modified arginine residues in αA-crystallin and found that replacing such arginine residues with alanine residues mimicked the effects of MGO on the chaperone function. Arginine 12 (R12 is a conserved amino acid residue in Hsp27 as well as αA- and αB-crystallin. When treated with MGO at or near physiological concentrations (2-10 µM, R12 was modified to hydroimidazolone in all three small heat shock proteins. In this study, we determined the effect of arginine substitution with alanine at position 12 (R12A to mimic MGO modification on the structure and chaperone function of these proteins. Among the three proteins, the R12A mutation improved the chaperone function of only αA-crystallin. This enhancement in the chaperone function was accompanied by subtle changes in the tertiary structure, which increased the thermodynamic stability of αA-crystallin. This mutation induced the exposure of additional client protein binding sites on αA-crystallin. Altogether, our data suggest that MGO-modification of the conserved R12 in αA-crystallin to hydroimidazolone may play an important role in reducing protein aggregation in the lens during aging and cataract formation.

Refractive lens exchange with a multifocal diffractive aspheric intraocular lens

Directory of Open Access Journals (Sweden)

Teresa Ferrer-Blasco

2012-06-01

Full Text Available PURPOSE: To evaluate the safety, efficacy and predictability after refractive lens exchange with multifocal diffractive aspheric intraocular lens implantation. METHODS: Sixty eyes of 30 patients underwent bilateral implantation with AcrySof® ReSTOR® SN6AD3 intraocular lens with +4.00 D near addition. Patients were divided into myopic and hyperopic groups. Monocular best corrected visual acuity at distance and near and monocular uncorrected visual acuity at distance and near were measured before and 6 months postoperatively. RESULTS: After surgery, uncorrected visual acuity was 0.08 ± 0.15 and 0.11 ± 0.14 logMAR for the myopic and hyperopic groups, respectively (50% and 46.67% of patients had an uncorrected visual acuity of 20/20 or better in the myopic and hyperopic groups, respectively. The safety and efficacy indexes were 1.05 and 0.88 for the myopic and 1.01 and 0.86 for the hyperopic groups at distance vision. Within the myopic group, 20 eyes remained unchanged after the surgery, and 3 gained >2 lines of best corrected visual acuity. For the hyperopic group, 2 eyes lost 2 lines of best corrected visual acuity, 21 did not change, and 3 eyes gained 2 lines. At near vision, the safety and efficacy indexes were 1.23 and 1.17 for the myopic and 1.16 and 1.13 for the hyperopic groups. Best corrected near visual acuity improved after surgery in both groups (from 0.10 logMAR to 0.01 logMAR in the myopic group, and from 0.10 logMAR to 0.04 logMAR in the hyperopic group. CONCLUSIONS: The ReSTOR® SN6AD3 intraocular lens in refractive lens exchange demonstrated good safety, efficacy, and predictability in correcting high ametropia and presbyopia.

21 CFR 886.5844 - Prescription spectacle lens.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Prescription spectacle lens. 886.5844 Section 886...) MEDICAL DEVICES OPHTHALMIC DEVICES Therapeutic Devices § 886.5844 Prescription spectacle lens. (a) Identification. A prescription spectacle lens is a glass or plastic device that is a lens intended to be worn by...

Unfolded-protein response-associated stabilization of p27(Cdkn1b) interferes with lens fiber cell denucleation, leading to cataract

Science.gov (United States)

Failure of lens fiber cell denucleation (LFCD) is associated with congenital cataracts, but the pathobiology awaits elucidation. Recent work has suggested that mechanisms that direct the unidirectional process of LFCD are analogous to the cyclic processes associated with mitosis. We found that lens-...

DNA mimic proteins: functions, structures, and bioinformatic analysis.

Science.gov (United States)

Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

2014-05-13

DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

Compare local pocket and global protein structure models by small structure patterns

KAUST Repository

Cui, Xuefeng; Kuwahara, Hiroyuki; Li, Shuai Cheng; Gao, Xin

2015-01-01

Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria

Optical fiber plasmonic lens for near-field focusing fabricated through focused ion beam

Science.gov (United States)

Sloyan, Karen; Melkonyan, Henrik; Moreira, Paulo; Dahlem, Marcus S.

2017-02-01

We report on numerical simulations and fabrication of an optical fiber plasmonic lens for near-field focusing applications. The plasmonic lens consists of an Archimedean spiral structure etched through a 100 nm-thick Au layer on the tip of a single-mode SM600 optical fiber operating at a wavelength of 632:8 nm. Three-dimensional finite-difference time-domain computations show that the relative electric field intensity of the focused spot increases 2:1 times when the number of turns increases from 2 to 12. Furthermore, a reduction of the intensity is observed when the initial inner radius is increased. The optimized plasmonic lens focuses light into a spot with a full-width at half-maximum of 182 nm, beyond the diffraction limit. The lens was fabricated by focused ion beam milling, with a 200nm slit width.

Plasma Lens for Muon and Neutrino Beams

International Nuclear Information System (INIS)

Kahn, S.A.; Korenev, S.; Bishai, M.; Diwan, M.; Gallardo, J.C.; Hershcovitch, A.; Johnson, B.M.

2008-01-01

The plasma lens is examined as an alternate to focusing horns and solenoids for use in a neutrino or muon beam facility. The plasma lens concept is based on a combined high-energy lens/target configuration. The current is fed at electrodes located upstream and downstream from the target where pion capturing is needed. The current flows primarily in the plasma, which has a lower resistivity than the target. A second plasma lens section, with an additional current feed, follows the target to provide shaping of the plasma for optimum focusing. The plasma lens is immersed in an additional solenoid magnetic field to facilitate the plasma stability. The geometry of the plasma is shaped to provide optimal pion capture. Simulations of this plasma lens system have shown a 25% higher neutrino production than the horn system. Plasma lenses have the additional advantage of negligible pion absorption and scattering by the lens material and reduced neutrino contamination during anti-neutrino running. Results of particle simulations using plasma lens will be presented

Wedged multilayer Laue lens

International Nuclear Information System (INIS)

Conley, Ray; Liu Chian; Qian Jun; Kewish, Cameron M.; Macrander, Albert T.; Yan Hanfei; Maser, Joerg; Kang, Hyon Chol; Stephenson, G. Brian

2008-01-01

A multilayer Laue lens (MLL) is an x-ray focusing optic fabricated from a multilayer structure consisting of thousands of layers of two different materials produced by thin-film deposition. The sequence of layer thicknesses is controlled to satisfy the Fresnel zone plate law and the multilayer is sectioned to form the optic. An improved MLL geometry can be created by growing each layer with an in-plane thickness gradient to form a wedge, so that every interface makes the correct angle with the incident beam for symmetric Bragg diffraction. The ultimate hard x-ray focusing performance of a wedged MLL has been predicted to be significantly better than that of a nonwedged MLL, giving subnanometer resolution with high efficiency. Here, we describe a method to deposit the multilayer structure needed for an ideal wedged MLL and report our initial deposition results to produce these structures

Solution structure and dynamics of melanoma inhibitory activity protein

International Nuclear Information System (INIS)

Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

2002-01-01

Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

Lens decenter and tilt measurement by interferogram

Science.gov (United States)

Hung, Min-Wei; Wu, Wen-Hong; Huang, Kuo-Cheng

2009-11-01

For the recent years, the vigorous development of the electro-optic industry, particularly the digital camera and the cellular phone camera, has placed a larger and larger demand for the optical devices. Among the optical lens, the aspherical optical lens plays the key component because the aspherical lens may provide better imaging quality then the spherical lens does. For the manufacturing reason, the aspherical lens is prone to a decenter or tilt issue with respect to the optical axes of its two surfaces. To measure decenter and tile error specifically would help to obviate the deficient lens, but most of the present measuring method can't provide this function. This paper proposed a new method to specifically measure the decenter and tile of lens by observing the interferogram of each surface. And the corresponding measuring instrument, which contains interferometer and motion stages, was introduced as well.

Clinical study of foldable intraocular lens secondary implantation after lens-vitrectomy in residual capsular with traumatic eyes

Directory of Open Access Journals (Sweden)

Ru-Fa Meng

2015-07-01

Full Text Available AIM: To investigate the operation methods and clinical effects of foldable intraocular lens secondary implantation after lens-vitrectomy in residual capsular with traumatic eyes.METHODS: During January 2012 to January 2014, foldable intraocular lens was implanted on 47 cases following lens-vitrectomy in residual capsular with traumatic eyes 3～6mo. Follow-up period was 6～12mo, averaged(8.21±2.63mo. RESULTS:All of 47 eyes had successful operation at one time, and position deviation was not appeared. The naked vision of the last postoperative follow-up was(0.44±0.19. Compared with best corrected visual acuity(0.41±0.23, and There was no significant difference between visual acuity of preoperative and last follow-up period(t=0.879, P=0.342. No severe complication was found. CONCLUSION: Secondary implantation of foldable intraocular lens is a safe and reliable method for correcting ametropia after lens-vitrectomy in residual capsular with traumatic eyes.

21 CFR 886.3600 - Intraocular lens.

Science.gov (United States)

2010-04-01

... DEVICES OPHTHALMIC DEVICES Prosthetic Devices § 886.3600 Intraocular lens. (a) Identification. An intraocular lens is a device made of materials such as glass or plastic intended to be implanted to replace the natural lens of an eye. (b) Classification. Class III. (c) Date PMA or notice of completion of a...

Improved protein surface comparison and application to low-resolution protein structure data

Directory of Open Access Journals (Sweden)

Kihara Daisuke

2010-12-01

Full Text Available Abstract Background Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM, which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs. The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. Results The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Conclusions Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.

Improved protein surface comparison and application to low-resolution protein structure data.

Science.gov (United States)

Sael, Lee; Kihara, Daisuke

2010-12-14

Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.

Topological properties of complex networks in protein structures

Science.gov (United States)

Kim, Kyungsik; Jung, Jae-Won; Min, Seungsik

2014-03-01

We study topological properties of networks in structural classification of proteins. We model the native-state protein structure as a network made of its constituent amino-acids and their interactions. We treat four structural classes of proteins composed predominantly of α helices and β sheets and consider several proteins from each of these classes whose sizes range from amino acids of the Protein Data Bank. Particularly, we simulate and analyze the network metrics such as the mean degree, the probability distribution of degree, the clustering coefficient, the characteristic path length, the local efficiency, and the cost. This work was supported by the KMAR and DP under Grant WISE project (153-3100-3133-302-350).

Studying Membrane Protein Structure and Function Using Nanodiscs

DEFF Research Database (Denmark)

Huda, Pie

The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

3D bioprinting of structural proteins.

Science.gov (United States)

Włodarczyk-Biegun, Małgorzata K; Del Campo, Aránzazu

2017-07-01

3D bioprinting is a booming method to obtain scaffolds of different materials with predesigned and customized morphologies and geometries. In this review we focus on the experimental strategies and recent achievements in the bioprinting of major structural proteins (collagen, silk, fibrin), as a particularly interesting technology to reconstruct the biochemical and biophysical composition and hierarchical morphology of natural scaffolds. The flexibility in molecular design offered by structural proteins, combined with the flexibility in mixing, deposition, and mechanical processing inherent to bioprinting technologies, enables the fabrication of highly functional scaffolds and tissue mimics with a degree of complexity and organization which has only just started to be explored. Here we describe the printing parameters and physical (mechanical) properties of bioinks based on structural proteins, including the biological function of the printed scaffolds. We describe applied printing techniques and cross-linking methods, highlighting the modifications implemented to improve scaffold properties. The used cell types, cell viability, and possible construct applications are also reported. We envision that the application of printing technologies to structural proteins will enable unprecedented control over their supramolecular organization, conferring printed scaffolds biological properties and functions close to natural systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

Science.gov (United States)

2014-01-01

We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

Developing the Regulatory Utility of the Exposome: Mapping Exposures for Risk Assessment through Lifestage Exposome Snapshots (LEnS).

Science.gov (United States)

Shaffer, Rachel M; Smith, Marissa N; Faustman, Elaine M

2017-08-07

Exposome-related efforts aim to document the totality of human exposures across the lifecourse. This field has advanced rapidly in recent years but lacks practical application to risk assessment, particularly for children's health. Our objective was to apply the exposome to children's health risk assessment by introducing the concept of Lifestage Exposome Snapshots (LEnS). Case studies are presented to illustrate the value of the framework. The LEnS framework encourages organization of exposome studies based on windows of susceptibility for particular target organ systems. Such analyses will provide information regarding cumulative impacts during specific critical periods of the life course. A logical extension of this framework is that regulatory standards should analyze exposure information by target organ, rather than for a single chemical only or multiple chemicals grouped solely by mechanism of action. The LEnS concept is a practical refinement to the exposome that accounts for total exposures during particular windows of susceptibility in target organ systems. Application of the LEnS framework in risk assessment and regulation will improve protection of children's health by enhancing protection of sensitive developing organ systems that are critical for lifelong health and well-being. https://doi.org/10.1289/EHP1250.

Impact of lens case hygiene guidelines on contact lens case contamination.

Science.gov (United States)

Wu, Yvonne T; Teng, Yuu Juan; Nicholas, Mary; Harmis, Najat; Zhu, Hua; Willcox, Mark D P; Stapleton, Fiona

2011-10-01

Lens case contamination is a risk factor for microbial keratitis. The effectiveness of manufacturers' lens case cleaning guidelines in limiting microbial contamination has not been evaluated in vivo. This study compared the effectiveness of manufacturers' guidelines and an alternative cleaning regimen. A randomized cross-over clinical trial with two phases (n = 40) was performed. Participants used the lens types of their choice in conjunction with the provided multipurpose solution (containing polyhexamethylene biguanide) for daily wear. In the manufacturers' guideline phase, cases were rinsed with multipurpose solution and air dried. In the alternative regimen phase, cases were rubbed, rinsed with solution, tissue wiped, and air-dried face down. The duration of each phase was 1 month. Lens cases were collected at the end of each phase for microbiological investigation. The levels of microbial contamination were compared, and compliance to both regimens was assessed. The case contamination rate was 82% (32/39) in the manufacturers' guideline group, compared with 72% (28/39) in the alternative regimen group. There were significantly fewer (p = 0.004) colony forming units (CFU) of bacteria from cases used by following the alternative regimen (CFU range of 0 to 10, and median of 12 CFU per well) compared with that of the manufacturer's guidelines (CFU range of 0 to 10, and median of 28 CFU per well). The compliance level between both guidelines was not significantly different (p > 0.05). The alternative guidelines are more effective in eliminating microbial contamination from lens cases than that of the current manufacturer's guideline. Simply incorporating rubbing and tissue-wiping steps in daily case hygiene reduces viable organism contamination.

21 CFR 886.1400 - Maddox lens.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Maddox lens. 886.1400 Section 886.1400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES OPHTHALMIC DEVICES Diagnostic Devices § 886.1400 Maddox lens. (a) Identification. A Maddox lens is a device...

Intracapsular lens extraction for the treatment of pupillary block glaucoma associated with anterior subluxation of the crystalline lens.

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Kim, Yong Joon; Ha, Seung Joo

2013-01-01

To report a case of pupillary block glaucoma associated with spontaneous crystalline lens subluxation into the anterior chamber in a 34-year-old man. Dry vitrectomy was performed for securing enough retrolental space, and an intracapsular lens extraction was then performed via a corneolimbal incision. Additional endothelial cell damage was avoided with an injection of viscoelastics and gentle extraction of the crystalline lens. After deepening of the anterior chamber, scleral fixation of the intraocular lens was performed with an ab externo technique. Two months after the operation, a well-fixated intraocular lens was observed and intraocular pressure was stable. The postoperative corneal astigmatism was -3.5 dpt, and the patient had a best-corrected visual acuity of 20/25. Postoperative complications included decreased endothelial cell count and sector iris paralysis near the incision site. An anteriorly subluxated crystalline lens can cause pupillary block glaucoma in healthy young adults. To prevent intraoperative complications, intracapsular lens extraction with dry vitrectomy can be a good surgical option. The endothelial cell density should be closely monitored after surgery.

Plasma Lens for Muon and Neutrino Beams

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Kahn, Stephen; Korenev, Sergey; Bishai, Mary; Diwan, Milind; Gallardo, Juan; Hershcovitch, Ady; Johnson, Brant

2008-04-01

The plasma lens is examined as an alternate to focusing horns and solenoids for use in a neutrino or muon beam facility. The plasma lens concept is based on a combined high-current lens/target configuration. The current is fed at electrodes located upstream and downstream from the target where pion capturing is needed. The current flows primarily in the plasma, which has a lower resistivity than the target. A second plasma lens section, with an additional current feed, follows the target to provide shaping of the plasma stability. The geometry of the plasma is shaped to provide optimal pion capture. Simulations of this plasma lens system have shown a 25% higher neutrino production than the horn system. A plasma lens has additional advantage: larger axial current than horns, minimal neutrino contamination during antineutrino running, and negligible pion absorption or scattering. Results from particle simulations using a plasma lens will be presented.

ProteinSplit: splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics

International Nuclear Information System (INIS)

Wyrwicz, Lucjan S; Koczyk, Grzegorz; Rychlewski, Leszek; Plewczynski, Dariusz

2007-01-01

The annotation of protein folds within newly sequenced genomes is the main target for semi-automated protein structure prediction (virtual structural genomics). A large number of automated methods have been developed recently with very good results in the case of single-domain proteins. Unfortunately, most of these automated methods often fail to properly predict the distant homology between a given multi-domain protein query and structural templates. Therefore a multi-domain protein should be split into domains in order to overcome this limitation. ProteinSplit is designed to identify protein domain boundaries using a novel algorithm that predicts disordered regions in protein sequences. The software utilizes various sequence characteristics to assess the local propensity of a protein to be disordered or ordered in terms of local structure stability. These disordered parts of a protein are likely to create interdomain spacers. Because of its speed and portability, the method was successfully applied to several genome-wide fold annotation experiments. The user can run an automated analysis of sets of proteins or perform semi-automated multiple user projects (saving the results on the server). Additionally the sequences of predicted domains can be sent to the Bioinfo.PL Protein Structure Prediction Meta-Server for further protein three-dimensional structure and function prediction. The program is freely accessible as a web service at http://lucjan.bioinfo.pl/proteinsplit together with detailed benchmark results on the critical assessment of a fully automated structure prediction (CAFASP) set of sequences. The source code of the local version of protein domain boundary prediction is available upon request from the authors

A hidden markov model derived structural alphabet for proteins.

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Camproux, A C; Gautier, R; Tufféry, P

2004-06-04

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

3D complex: a structural classification of protein complexes.

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Emmanuel D Levy

2006-11-01

Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Identification of similar regions of protein structures using integrated sequence and structure analysis tools

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Heiland Randy

2006-03-01

Full Text Available Abstract Background Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. Results Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. Conclusion With structural genomics initiatives determining structures with little, if any, functional characterization

A wide-angle gradient index optical model of the crystalline lens and eye of the octopus.

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Jagger, W S; Sands, P J

1999-08-01

Cephalopods and fish have had no common ancestor since the Cambrian, and their eyes are a classic example of convergent evolution. The octopus has no cornea, and immerson renders the trout cornea optically ineffective. As a result, the nearly spherical lens is responsible for all refraction in these eyes. In spite of the fact that the octopus lens consists of two joined parts, while the trout lens consists of one part, we show here that their optical properties are very similar. An index gradient bends rays within these lenses, adding power and correcting spherical aberration. High spherical symmetry in both lenses strongly reduces other monochromatic aberrations and yields a wide field of vision, advantageous in attack and evasion. The octopus Mattheissen's ratio, 2.83, an inverse measure of light-gathering power, lies above the trout value of 2.38 but within the range of values reported for fish. Strong uncorrected longitudinal chromatic aberration is nearly identical in both animals as a result of similar lens protein optical properties, and will limit resolution. We discuss how animal lifestyle requirements and lens material properties influence the design of these eyes.

Simulation of light propagation in the thin-film waveguide lens

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Malykh, M. D.; Divakov, D. V.; Sevastianov, L. A.; Sevastianov, A. L.

2018-04-01

In this paper we investigate the solution of the problem of modeling the propagation of electromagnetic radiation in three-dimensional integrated optical structures, such as waveguide lenses. When propagating through three-dimensional waveguide structures the waveguide modes can be hybridized, so the mathematical model of their propagation must take into account the connection of TE- and TM-mode components. Therefore, an adequate consideration of hybridization of the waveguide modes is possible only in vector formulation of the problem. An example of three-dimensional structure that hybridizes waveguide modes is the Luneburg waveguide lens, which also has focusing properties. If the waveguide lens has a radius of the order of several tens of wavelengths, its variable thickness at distances of the order of several wavelengths is almost constant. Assuming in this case that the electromagnetic field also varies slowly in the direction perpendicular to the direction of propagation, one can introduce a small parameter characterizing this slow varying and decompose the solution in powers of the small parameter. In this approach, in the zeroth approximation, scalar diffraction problems are obtained, the solution of which is less resource-consuming than the solution of vector problems. The calculated first-order corrections of smallness describe the connection of TE- and TM-modes, so the solutions obtained are weakly-hybridized modes. The formulation of problems and methods for their numerical solution in this paper are based on the authors' research on waveguide diffraction on a lens in a scalar formulation.

L-type calcium channels play a critical role in maintaining lens transparency by regulating phosphorylation of aquaporin-0 and myosin light chain and expression of connexins.

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Maddala, Rupalatha; Nagendran, Tharkika; de Ridder, Gustaaf G; Schey, Kevin L; Rao, Ponugoti Vasantha

2013-01-01

Homeostasis of intracellular calcium is crucial for lens cytoarchitecture and transparency, however, the identity of specific channel proteins regulating calcium influx within the lens is not completely understood. Here we examined the expression and distribution profiles of L-type calcium channels (LTCCs) and explored their role in morphological integrity and transparency of the mouse lens, using cDNA microarray, RT-PCR, immunoblot, pharmacological inhibitors and immunofluorescence analyses. The results revealed that Ca (V) 1.2 and 1.3 channels are expressed and distributed in both the epithelium and cortical fiber cells in mouse lens. Inhibition of LTCCs with felodipine or nifedipine induces progressive cortical cataract formation with time, in association with decreased lens weight in ex-vivo mouse lenses. Histological analyses of felodipine treated lenses revealed extensive disorganization and swelling of cortical fiber cells resembling the phenotype reported for altered aquaporin-0 activity without detectable cytotoxic effects. Analysis of both soluble and membrane rich fractions from felodipine treated lenses by SDS-PAGE in conjunction with mass spectrometry and immunoblot analyses revealed decreases in β-B1-crystallin, Hsp-90, spectrin and filensin. Significantly, loss of transparency in the felodipine treated lenses was preceded by an increase in aquaporin-0 serine-235 phosphorylation and levels of connexin-50, together with decreases in myosin light chain phosphorylation and the levels of 14-3-3ε, a phosphoprotein-binding regulatory protein. Felodipine treatment led to a significant increase in gene expression of connexin-50 and 46 in the mouse lens. Additionally, felodipine inhibition of LTCCs in primary cultures of mouse lens epithelial cells resulted in decreased intracellular calcium, and decreased actin stress fibers and myosin light chain phosphorylation, without detectable cytotoxic response. Taken together, these observations reveal a crucial

[Representation and mathematical analysis of human crystalline lens].

Science.gov (United States)

Tălu, Stefan; Giovanzana, Stefano; Tălu, Mihai

2011-01-01

The surface of human crystalline lens can be described and analyzed using mathematical models based on parametric representations, used in biomechanical studies and 3D solid modeling of the lens. The mathematical models used in lens biomechanics allow the study and the behavior of crystalline lens on variables and complex dynamic loads. Also, the lens biomechanics has the potential to improve the results in the development of intraocular lenses and cataract surgery. The paper presents the most representative mathematical models currently used for the modeling of human crystalline lens, both optically and biomechanically.

[Intraocular lens implantation with one loop haptic amputated: a new propose to the subluxation lens surgical treatment].

Science.gov (United States)

Ventura, Marcelo; Endriss, Daniela

2010-01-01

To evaluate the postoperative results of congenital lens subluxation corrected by a new technique. Retrospective chart review of 21 eyes of 13 patients with no traumatic lens subluxation who underwent surgery in Altino Ventura Foundation from April, 1999 to April, 2004. The mean age was 8.7 +/- 5.4 years old, and the mean follow-up period was 21.5 +/- 19.3 months. Patients underwent phacoaspiration, endocapsular ring and intraocular lens (IOL) implantation. The implanted IOL had one loop haptic excised and was supported above the ring, inside the capsular bag promoting intraocular lens centralization. Visual acuity improvement was observed in all cases. There was a significant reduction of the spherical equivalent and spherical component comparing the pre and postoperative refraction (psubluxation surgical treatment, promoting lens centralization and postoperative visual acuity improvement.

Deprotonated imidodiphosphate in AMPPNP-containing protein structures

International Nuclear Information System (INIS)

Dauter, Miroslawa; Dauter, Zbigniew

2011-01-01

In certain AMPPNP-containing protein structures, the nitrogen bridging the two terminal phosphate groups can be deprotonated. Many different proteins utilize the chemical energy provided by the cofactor adenosine triphosphate (ATP) for their proper function. A number of structures in the Protein Data Bank (PDB) contain adenosine 5′-(β,γ-imido)triphosphate (AMPPNP), a nonhydrolysable analog of ATP in which the bridging O atom between the two terminal phosphate groups is substituted by the imido function. Under mild conditions imides do not have acidic properties and thus the imide nitrogen should be protonated. However, an analysis of protein structures containing AMPPNP reveals that the imide group is deprotonated in certain complexes if the negative charges of the phosphate moieties in AMPPNP are in part neutralized by coordinating divalent metals or a guanidinium group of an arginine

Fragger: a protein fragment picker for structural queries.

Science.gov (United States)

Berenger, Francois; Simoncini, David; Voet, Arnout; Shrestha, Rojan; Zhang, Kam Y J

2017-01-01

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins.

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Pietro Scaturro

Full Text Available Non-structural protein 1 (NS1 is one of the most enigmatic proteins of the Dengue virus (DENV, playing distinct functions in immune evasion, pathogenesis and viral replication. The recently reported crystal structure of DENV NS1 revealed its peculiar three-dimensional fold; however, detailed information on NS1 function at different steps of the viral replication cycle is still missing. By using the recently reported crystal structure, as well as amino acid sequence conservation, as a guide for a comprehensive site-directed mutagenesis study, we discovered that in addition to being essential for RNA replication, DENV NS1 is also critically required for the production of infectious virus particles. Taking advantage of a trans-complementation approach based on fully functional epitope-tagged NS1 variants, we identified previously unreported interactions between NS1 and the structural proteins Envelope (E and precursor Membrane (prM. Interestingly, coimmunoprecipitation revealed an additional association with capsid, arguing that NS1 interacts via the structural glycoproteins with DENV particles. Results obtained with mutations residing either in the NS1 Wing domain or in the β-ladder domain suggest that NS1 might have two distinct functions in the assembly of DENV particles. By using a trans-complementation approach with a C-terminally KDEL-tagged ER-resident NS1, we demonstrate that the secretion of NS1 is dispensable for both RNA replication and infectious particle production. In conclusion, our results provide an extensive genetic map of NS1 determinants essential for viral RNA replication and identify a novel role of NS1 in virion production that is mediated via interaction with the structural proteins. These studies extend the list of NS1 functions and argue for a central role in coordinating replication and assembly/release of infectious DENV particles.

Changes of enzyme activities in lens after glaucoma trabecular resection

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Jian-Ping Wang

2013-08-01

Full Text Available AIM: To observe the change of lens antioxidant enzyme activity after glaucoma trabecular resection. METHODS: Thirty-two eyes of sixteen New-Zealand rabbits(2.2-2.4kgwere divided into two groups. The left eyes of rabbits underwent standard glaucoma trabecular resection were treatment group, and the normal right eyes served as controls. Transparency of lenses was monitored by a slit-lamp biomicroscopy before and after glaucoma trabecular resection. The morphology of lens cells was observed under the light microscope.The activities of Na+-K+-ATPase,catalase(CAT, glutathion peroxidase(GSH-px, glutathione reductase(GR, superoxide dismutase(SODand content of malondialdehyde(MDAin lenses were detected six months after trabecular resection. RESULTS: Lenses were clear in both treatment group and normal control group during the six months after operation. The morphology and structure of lens cells were normal under the light microscope in both operation group and normal group. The activity of lens cells antioxidant enzyme activity were significantly decreased in operation group compared with control group, Na+-K+-ATPase declined by 20.97%, CAT declined by 16.36%, SOD declined by 4.46%, GR declined by 4.85%, GSH-px declined by 10.02%, and MDA increased by 16.31%. CONCLUSION: Glaucoma trabecular resection can induce the change of Na+-K+-ATPase, CAT, GSH-px, GR, SOD and MDA in lens of rabbit. Glaucoma filtration surgery for the occurrence of cataract development mechanism has important guiding significance.

A balance of FGF and BMP signals regulates cell cycle exit and Equarin expression in lens cells

Science.gov (United States)

Jarrin, Miguel; Pandit, Tanushree; Gunhaga, Lena

2012-01-01

In embryonic and adult lenses, a balance of cell proliferation, cell cycle exit, and differentiation is necessary to maintain physical function. The molecular mechanisms regulating the transition of proliferating lens epithelial cells to differentiated primary lens fiber cells are poorly characterized. To investigate this question, we used gain- and loss-of-function analyses to modulate fibroblast growth factor (FGF) and/or bone morphogenetic protein (BMP) signals in chick lens/retina explants. Here we show that FGF activity plays a key role for proliferation independent of BMP signals. Moreover, a balance of FGF and BMP signals regulates cell cycle exit and the expression of Ccdc80 (also called Equarin), which is expressed at sites where differentiation of lens fiber cells occurs. BMP activity promotes cell cycle exit and induces Equarin expression in an FGF-dependent manner. In contrast, FGF activity is required but not sufficient to induce cell cycle exit or Equarin expression. Furthermore, our results show that in the absence of BMP activity, lens cells have increased cell cycle length or are arrested in the cell cycle, which leads to decreased cell cycle exit. Taken together, these findings suggest that proliferation, cell cycle exit, and early differentiation of primary lens fiber cells are regulated by counterbalancing BMP and FGF signals. PMID:22718906

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

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Srinivasan Narayanaswamy

2010-06-01

Full Text Available Abstract Background Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. Results In the present analysis, starting from Cα positions of low resolution cryo electron microscopic structures the residue level details of protein-protein interaction interfaces of dengue virus coat proteins have been predicted. By comparing the preexisting structures of virus in different phases of life cycle, the changes taking place in these predicted protein-protein interaction interfaces were followed as a function of maturation process of the virus. Besides changing the current notion about the presence of only homodimers in the mature viral coat, the present analysis indicated presence of a proline-rich motif at the protein-protein interaction interface of the coat protein. Investigating the conservation status of these seemingly functionally crucial residues across other members of flaviviridae family enabled dissecting common mechanisms used for infections by these viruses. Conclusions Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens.

De novo protein structure determination using sparse NMR data

International Nuclear Information System (INIS)

Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

2000-01-01

We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

A medieval fallacy: the crystalline lens in the center of the eye.

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Leffler, Christopher T; Hadi, Tamer M; Udupa, Akrithi; Schwartz, Stephen G; Schwartz, Daniel

2016-01-01

To determine whether, as most modern historians have written, ancient Greco-Roman authors believed the crystalline lens is positioned in the center of the eye. Historians have written that statements about cataract couching by Celsus, or perhaps Galen of Pergamon, suggested a centrally located lens. Celsus specifically wrote that a couching needle placed intermediate between the corneal limbus and the lateral canthus enters an empty space, presumed to represent the posterior chamber. Ancient ophthalmic literature was analyzed to understand where these authors believed the crystalline lens was positioned. In order to estimate where Celsus proposed entering the eye during couching, we prospectively measured the distance from the temporal corneal limbus to the lateral canthus in 30 healthy adults. Rufus of Ephesus and Galen wrote that the lens is anterior enough to contact the iris. Galen wrote that the lens equator joins other ocular structures at the corneoscleral junction. In 30 subjects, half the distance from the temporal corneal limbus to the lateral canthus was a mean of 4.5 mm (range: 3.3-5.3 mm). Descriptions of couching by Celsus and others are consistent with pars plana entry of the couching needle. Anterior angulation of the needle would permit contact of the needle with the lens. Ancient descriptions of anatomy and couching do not establish the microanatomic relationships of the ciliary region with any modern degree of accuracy. Nonetheless, ancient authors, such as Galen and Rufus, clearly understood that the lens is located anteriorly. There is little reason to believe that Celsus or other ancient authors held a variant understanding of the anatomy of a healthy eye. The notion of the central location of the lens seems to have arisen with Arabic authors in 9th century Mesopotamia, and lasted for over 7 centuries.

Structural studies of human glioma pathogenesis-related protein 1

Energy Technology Data Exchange (ETDEWEB)

Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu [College of Medicine, Nebraska Medical Center, Omaha, NE 68198-6495 (United States); Koski, Raymond A.; Bonafé, Nathalie [L2 Diagnostics LLC, 300 George Street, New Haven, CT 06511 (United States); College of Medicine, Nebraska Medical Center, Omaha, NE 68198-6495 (United States)

2011-10-01

Structural analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1, a membrane protein implicated in the proliferation of aggressive brain cancer, is presented. Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn{sup 2+} complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn{sup 2+} similarly to snake-venom CRISPs, which are involved in Zn{sup 2+}-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

Constraint Logic Programming approach to protein structure prediction

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Fogolari Federico

2004-11-01

Full Text Available Abstract Background The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. Conclusions The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

Constraint Logic Programming approach to protein structure prediction.

Science.gov (United States)

Dal Palù, Alessandro; Dovier, Agostino; Fogolari, Federico

2004-11-30

The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

Bioinspired adaptive gradient refractive index distribution lens

Science.gov (United States)

Yin, Kezhen; Lai, Chuan-Yar; Wang, Jia; Ji, Shanzuo; Aldridge, James; Feng, Jingxing; Olah, Andrew; Baer, Eric; Ponting, Michael

2018-02-01

Inspired by the soft, deformable human eye lens, a synthetic polymer gradient refractive index distribution (GRIN) lens with an adaptive geometry and focal power has been demonstrated via multilayer coextrusion and thermoforming of nanolayered elastomeric polymer films. A set of 30 polymer nanolayered films comprised of two thermoplastic polyurethanes having a refractive index difference of 0.05 were coextruded via forced-assembly technique. The set of 30 nanolayered polymer films exhibited transmission near 90% with each film varying in refractive index by 0.0017. An adaptive GRIN lens was fabricated from a laminated stack of the variable refractive index films with a 0.05 spherical GRIN. This lens was subsequently deformed by mechanical ring compression of the lens. Variation in the optical properties of the deformable GRIN lens was determined, including 20% variation in focal length and reduced spherical aberration. These properties were measured and compared to simulated results by placido-cone topography and ANSYS methods. The demonstration of a solid-state, dynamic focal length, GRIN lens with improved aberration correction was discussed relative to the potential future use in implantable devices.

PSPP: a protein structure prediction pipeline for computing clusters.

Directory of Open Access Journals (Sweden)

Michael S Lee

2009-07-01

Full Text Available Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML formats. So far, the pipeline has been used to study viral and bacterial proteomes.The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform