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The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.

Bacterial cellulose (BC) is a natural polymer that has a number of unique properties that determine the need to synthesize large amounts of it and to search the ways to increase the productivity of strains and to optimize the nutritive media. It is known that the choice of the producer for BC synthesis has an impact on its final properties and on the productivity of this polymer production. Under static liquid phase cultivation conditions, all cellulose-producing bacteria form a uniform film on the medium surface that serves as a scaffold for cells immobilization, thus providing them with the access to the air/liquid interface, where the access to oxygen is not limited. Meanwhile, when cultivation goes under agitating conditions, most of Gluconacetobacter xylinus strains produce less cellulose in form of globules of various sizes, despite the better oxygen access. Several authors explain the lower cellulose outcome when cultivated under agitated conditions by the appearance of spontaneous mutants that do not produce cellulose in the population. It was revealed that when grown on agarized media, cellulosenon- producing mutants form colonies of a specific mucoid type, while non-mucoid phenotype cells form smooth colonies of non-mucoid type. To our knowledge, there is no published research on the impact of cultivation conditions and nutritive medium composition on the appearance of spontaneous phenotype mutations in the population of Gluconacetobacter hansenii representatives. The aim of the present research is to elucidate the impact of the carbon source on the productivity of G. hansenii strain and the appearance of cellulose-negative mutants under static cultivation conditions. We studied the strain G. hansenii GH 1/2008 (VKPM В-10547) as a BC source. Liquid phase static cultivation of G. hansenii GH 1/2008 was carried out using the modified Hestrin-Schramm (HS) medium, containing 4% of monosaccharides (glucose, fructose and galactose) or disaccharides (sucrose, maltose, lactose) as carbon sources. The occurrence of mutants was calculated considering phenotypes of colonies obtained by seeding the samples of cultural liquid and wash-offs of cells from films produced by the cultivation of the producer on modified agarized HS media. The polymer outcome was expressed as the film absolute dry weight (a.d.w.) per cultivation medium volume unit. We studied the morphology of the producer’s wild type and mutant cells by means of atomic force microscopy (AFM) (See Fig. 8). The structural organization of the produced films and gel was revealed by means of scanning electron microscopy (SEM) performed after freeze-drying. The composition of the fibers was checked acquiring FTIR Spectroscopy. We established that G. hansenii GH 1/2008 produces a dense film on media containing fructose, glucose and sucrose, while the polymer has gel consistence when grown on maltose, galactose and lactose (See Fig. 1). The maximal quantity (a.d.w.) of polymer was produced on fructose- and sucrose-containing media. The overall number of immobilized producer cells was considerably higher when grown on media with glucose, fructose and sucrose than on gels grown on those containing maltose, galactose and lactose (See Table 1). SEM imaging revealed considerable difference in the microscale organization of films and gels produced by G. hansenii GH 1/2008 on various carbon sources (See Fig. 2). Fructose-containing medium yields the densest structure with dense layers separated by 2μm thick areas filled with non-ordered BC fibrils. The microscale organization of sucrose- and glucose-based films were very similar and had a cell-like structure. In cases where the synthesized polymer had squeezable gel consistence, its microstructure was not layered but close to isotropic. The studies of gels by means of FTIR spectroscopy showed that the gels are also formed of BC molecules; the spectra were almost identical (See Fig. 4). The only difference, i.e. the intensity of the 1638 см-1 peak, can be explained by the presence of a higher amount of bound water in the latter. It is known that some strains of this species may produce glucuronic acid oligomers under unfavorable conditions, but peaks corresponding to carboxyl or carbonyl groups were not revealed in the spectra. This is the evidence that no detectable amounts of glucuronic acid were produced under conditions studied. The analysis of colonies of G. hansenii GH 1/2008 cultivated under static conditions on media containing various carbon sources revealed colonies with two dominating phenotypes: non-mucoid smooth convex colonies and mucoid flat ones (See Fig. 5). The number of cells forming smooth non-mucoid colonies on agarized media was maximal in the inoculations of cultural liquids after the cultivation on media containing fructose and sucrose, i.e. those carbon sources that demonstrated high productivity per 1L of cultural liquid (See Fig. 6). In the inoculations of the cultural liquid and wash-offs of cells immobilized on gels obtained by the cultivation on media containing galactose and lactose, the number of mucoid colonies was considerably higher (See Table 2). The clones forming mucoid type colonies did not produce BC films when reinoculated in liquid media, while those forming colonies of mucoid (smooth) type produce films on the 3rd day of cultivation (See Fig. 7). The analysis of cells shape and sizes by means of AFM did not reveal any statistically valid difference between the mutants and the wild type. The present research shows that the source of carbon is a selective factor in the formation of the inner composition of the population of clones of the bacterial cellulose producer Gluconacetobacter hansenii GH 1/2008. The proliferation of cellulosenegative cells arouses competition for the substrate with cellulose-positive cells of G. hansenii GH 1/2008 that reduces the number of the latter and the production of the exopolymer.

Lipofuscin granules accumulate in the retinal pigment epithelium (RPE) with age, especially in patients with visual diseases, including progressive age-related macular degeneration (AMD). Bisretinoids and their photooxidation and photodegradation products are major sources of lipofuscin granule fluorescence. The present study focused on examining the fluorescence decay characteristics of bisretinoid photooxidation and photodegradation products to evaluate the connection between fluorescence lifetime and spectral characteristics of target fluorophore groups. The primary objective of the study was to apply experimental spectral analysis results of lipofuscin granule fluorescence properties to interpretation of fluorescence lifetime imaging ophthalmoscopy data. Fluorescence analysis of the lipofuscin granule fluorophores in RPE collected from cadaver eyes was performed. The fluorescence lifetimes were measured by picosecond-resolved time correlated single photon counting technique. A global analytical method was applied to analyze data sets. The photooxidation and photodegradation products of bisretinoids exhibited a longer fluorescence lifetime (average value approximately 6 ns) and a shorter wavelength maximum (530–580 nm). Further, these products significantly contributed (more than 30%), to total fluorescence compared to the other fluorophores in lipofuscin granules. Thus, the contribution of oxidized lipofuscin bisretinoids to autofluorescence decay kinetics is an important characteristic for fluorescence lifetime imaging microscopy data analysis. The higher average fluorescence lifetime in AMD eyes was likely due to the higher abundance of oxidized bisretinoids compared with non-oxidized bisretinoids. Because higher level of oxidized bisretinoids is indicative of pathological processes in the retina and RPE, the present findings have the potential to improve fluorescence lifetime imaging approaches for early diagnosis of degenerative processes in the retina and RPE.

The objective of this study was screening of ommochromes from the compound eyes of insects and comparison of their antioxidant properties. Ommochromes were isolated in preparative quantities from insects of five different families: Stratiomyidae, Sphingidae, Blaberidae, Acrididae, and Tenebrionidae. The yield of ommochromes (dry pigment weight) was 0.9-5.4% of tissue wet weight depending on the insect species. Isolated pigments were analyzed by high-performance liquid chromatography and represented a mixture of several ommochromes of the ommatin series. The isolated ommochromes displayed a pronounced fluorescence with the emission maxima at 435-450 nm and 520-535 nm; furthermore, the emission intensity increased significantly upon ommochrome oxidation with hydrogen peroxide. The ommochromes produced a stable EPR signal consisting of a singlet line with g = 2.0045-2.0048, width of 1.20-1.27 mT, and high concentration of paramagnetic centers (> 1017 spin/g dry weight). All the investigated ommochromes demonstrated high antiradical activity measured from the degree of chemiluminescence quenching in a model system containing luminol, hemoglobin, and hydrogen peroxide. The ommochromes strongly inhibited peroxidation of the photoreceptor cell outer segments induced by visible light in the presence of lipofuscin granules from the human retinal pigment epithelium, as well as suppressed iron/ascorbate-mediated lipid peroxidation. The obtained results are important for understanding the biological functions of ommochromes in invertebrates and identifying invertebrate species that could be used as efficient sources of ommochromes for pharmacological preparations to prevent and treat pathologies associated with the oxidative stress development.

A global analysis of the fluorescence decay kinetics of a chloroform extract of lipofuscin granules from the retinal pigment epithelium cells of human cadaver eyes is performed. The analysis makes it possible to reconstruct the individual fluorescence properties of four groups of fluorophores belonging to bisretinoids and the products of their photooxidation and photodegradation. The characteristic fluorescence lifetimes are correlated with the spectral characteristics of the indicated fluorophore groups using the averaged spectral and kinetic characteristics of the chloroform extract.

We have studied dark-adaptation at three levels in the eyes of the crustacean Mysis relicta over 2–3 weeks after exposing initially dark-adapted animals to strong white light: regeneration of 11-cis retinal through the retinoid cycle (by HPLC), restoration of native rhodopsin in photoreceptor membranes (by MSP), and recovery of eye photosensitivity (by ERG). We compare two model populations (“Sea”, Sp, and “Lake”, Lp) inhabiting, respectively, a low light and an extremely dark environment. 11-cis retinal reached 60–70% of the pre-exposure levels after 2 weeks in darkness in both populations. The only significant Lp/Sp difference in the retinoid cycle was that Lp had much higher levels of retinol, both basal and light-released. In Sp, rhodopsin restoration and eye photoresponse recovery parallelled 11-cis retinal regeneration. In Lp, however, even after 3 weeks only ca. 25% of the rhabdoms studied had incorporated new rhodopsin, and eye photosensitivity showed only incipient recovery from severe depression. The absorbance spectra of the majority of the Lp rhabdoms stayed constant around 490–500 nm, consistent with metarhodopsin II dominance. We conclude that sensitivity recovery of Sp eyes was rate-limited by the regeneration of 11-cis retinal, whilst that of Lp eyes was limited by inertia in photoreceptor membrane turnover.

PURPOSE: The aim of this work is the determination of quantitative diagnostic criteria based on the spectral characteristics of fundus autofluorescence to detect early stages of degeneration in the retina and retinal pigment epithelium (RPE). METHODS: RPE cell suspension samples were obtained from the cadaver eyes with and without signs of age-related macular degeneration (AMD). Fluorescence analysis at an excitation wavelength of 488 nm was performed. The fluorescence lifetimes of lipofuscin-granule fluorophores were measured by counting time-correlated photon method. RESULTS: Comparative analysis of fluorescence spectra of RPE cell suspensions from the cadaver eyes with and without signs of AMD showed a significant difference in fluorescence intensity at 530–580 nm in response to fluorescence excitation at 488 nm. It was notably higher in eyes with visual pathology than in normal eyes regardless of the age of the eye donor. Measurements of fluorescence lifetimes of lipofuscin fluorophores showed that the contribution of photooxidation and photodegradation products of bisretinoids to the total fluorescence at 530–580 nm of RPE cell suspensions was greater in eyes with visual pathology than in normal eyes. CONCLUSION: Because photooxidation and photodegradation products of bisretinoids are markers of photodestructive processes, which can cause RPE cell death and initiate degenerative processes in the retina, quantitative determination of increases in these bisretinoid products in lipofuscin granules may be used to establish quantitative diagnostic criteria for degenerative processes in the retina and RPE.

The presence of carotenoids in the vitreous body, retina, lens, retinal pigment epithelium together with choroid (hereinafter RPE), and ciliary body and iris together with choroidal stroma (hereinafter CBI) was studied throughout the second trimester of prenatal development of the human eye. It has been found that the vitreous body, retina, and RPE contain lutein and its oxidized forms. Zeaxanthin was not found in the tissues studied. The presence of lutein in the vitreous body is transient and no longer detected after 28 weeks of gestation. Lutein was not detected in the lens and CBI, but its oxidized forms were found. The presence of carotenoids in different tissues of the eye in the course of normal eye development and the antioxidant role of carotenoids are discussed.

A quantum-classical model of photoisomerization of the visual pigment rhodopsin chromophore is proposed. At certain (and more realistic) parameter value combinations, the model is shown to accurately reproduce a number of independent experimental data on the photoreaction dynamics: the quantum yield, the time to reach the point of conical intersection of potential energy surfaces, the termination time of the evolution of quantum subsystem, as well as the characteristic low frequencies of retinal molecular lattice fluctuations during photoisomerization. In addition, the model behavior is in good accordance with experimental data about coherence and local character of quantum transition.

A modified model of the rhodopsin retinal chromophore cis–trans photoisomerization is developed, where the electron-vibration coupling constant depends exponentially on displacements of mass points. The quantum subsystem of the model includes three electronic states for rhodopsin: (i) the ground state, (ii) the excited state, (iii) the primary photoproduct in the ground state. The classical subsystem includes three mass points. The modifications give sufficient improvement of agreement between computational data and experiments, with all parameters of the model being very close to the most physically realistic values. In particular, improvements concern with data on residual coherent oscillations after photoisomerization is complete.

The supramolecular organization of the visual pigment rhodopsin in the photoreceptor membrane remains contentious. Specifically, whether this G protein-coupled receptor functions as a monomer or dimer remains unknown, as does the presence or absence of ordered packing of rhodopsin molecules in the photoreceptor membrane. Completely opposite opinions have been expressed on both issues. Herein, using small-angle neutron and X-ray scattering approaches, we performed a comparative analysis of the structural characteristics of the photoreceptor membrane samples in buffer, both in the outer segment of photoreceptor cells, and in the free photoreceptor disks. The average distance between the centers of two neighboring rhodopsin molecules was found to be ~5.8 nm in both cases. The results indicate an unusually high packing density of rhodopsin molecules in the photoreceptor membrane, but molecules appear to be randomly distributed in the membrane without any regular ordering.

Influences of alkali or alkaline earth sulfates on the hydration of cubic tricalcium aluminate (C3A) were evaluated by in situ dissolution rate measurements, by ex situ near-surface composition measurements with secondary ion mass spectrometry, and by in situ synchrotron X-ray diffraction to monitor precipitation of hydration products. Both slight reductions in dissolution rate and cation-specific interactions with the solid were observed. The near-surface Ca/Al ratio is significantly lower after some dissolution and the electrolyte cations are incorporated within the surface with different affinities (Mg2+ > K+ > Na+). An interfacial dissolution-reprecipitation mechanism may explain the observations as well as, or better than, a simple cation exchange. The sulfate concentration in solution affects the rates of both C3A dissolution and precipitation of hydration products. Sulfate ions likely adsorb at the hydrous Al-rich surface layer, thereby reducing the dissolution rate of aluminates and delaying the precipitation of aluminate hydration products.

It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software.

Anion-selective opsins slow ChloC and ACR2 were expressed in rat brain cortical neurons by electroporation in utero. It is shown that the light-activated channel ACR2 has pronounced advantages in terms of both the inactivation kinetics and the neuron inhibition intensity, which is associated with a more negative value of the light-activated current reversal potential compared to the slow ChloC channel. The identified properties of opsin ACR2 indicate that it can be used for strictly controlled suppression of neuronal activity in optogenetic experiments, including the expression in the retinal ganglionic cells for reconstituting the OFF-component of their receptive field, which is essential for optogenetic prosthetics of degenerative retina.

Significance Adipocyte differentiation is necessary for metabolic homeostasis. Transcription factors control adipocyte differentiation by regulating expression of genes required for adipocyte function. Here we show that the bromodomain and extraterminal domain (BET) family of bromodomain-containing proteins are important coregulators of adipogenesis. BRD4 binds to enhancers that drive expression of PPARγ, a master transcription factor required for normal adipocyte differentiation. Disrupting BRD4 at these enhancers blocks PPARγ expression and impairs differentiation. Understanding the molecular determinants of PPARγ expression and adipocyte differentiation may provide insights into the pathogenesis of metabolic diseases related to adipose tissue dysfunction and obesity. Furthermore, these data implicate metabolic pathways and their transcriptional regulators as potential targets of BET bromodomain inhibitors, as currently under investigation in human clinical trials of cancer therapy., Developmental transitions are guided by master regulatory transcription factors. During adipogenesis, a transcriptional cascade culminates in the expression of PPARγ and C/EBPα, which orchestrate activation of the adipocyte gene expression program. However, the coactivators controlling PPARγ and C/EBPα expression are less well characterized. Here, we show the bromodomain-containing protein, BRD4, regulates transcription of PPARγ and C/EBPα. Analysis of BRD4 chromatin occupancy reveals that induction of adipogenesis in 3T3L1 fibroblasts provokes dynamic redistribution of BRD4 to de novo super-enhancers proximal to genes controlling adipocyte differentiation. Inhibition of the bromodomain and extraterminal domain (BET) family of bromodomain-containing proteins impedes BRD4 occupancy at these de novo enhancers and disrupts transcription of Pparg and Cebpa, thereby blocking adipogenesis. Furthermore, silencing of these BRD4-occupied distal regulatory elements at the Pparg locus by CRISPRi demonstrates a critical role for these enhancers in the control of Pparg gene expression and adipogenesis in 3T3L1s. Together, these data establish BET bromodomain proteins as time- and context-dependent coactivators of the adipocyte cell state transition.

Photochemical reaction dynamics of the primary events in recombinant bacteriorhodopsin (bRrec) was studied by femtosecond laser absorption spectroscopy with 25-fs time resolution. bRrec was produced in an Escherichia coli expression system. Since bRrec was prepared in a DMPC–CHAPS micelle system in the monomeric form, its comparison with trimeric and monomeric forms of the native bacteriorhodopsin (bRtrim and bRmon, respectively) was carried out. We found that bRrec intermediate I (excited state of bR) was formed in the range of 100 fs, as in the case of bRtrim and bRmon. Further processes, namely the decay of the excited state I and the formation of intermediates J and K of bRrec, occurred more slowly compared to bRtrim, but similarly to bRmon. The lifetime of intermediate I, judging from the signal of ΔA ESA(470-480 nm), was 0.68 ps (78%) and 4.4 ps (22%) for bRrec, 0.52 ps (73%) and 1.7 ps (27%) for bRmon, and 0.45 ps (90%) and 1.75 ps (10%) for bRtrim. The formation time of intermediate K, judging from the signal of ΔA GSA(625-635 nm), was 13.5 ps for bRrec, 9.8 ps for bRmon, and 4.3 ps for bRtrim. In addition, there was a decrease in the photoreaction efficiency of bRrec and bRmon as seen by a decrease in absorbance in the differential spectrum of the intermediate K by ~14%. Since photochemical properties of bRrec are similar to those of the monomeric form of the native protein, bRrec and its mutants can be considered as a basis for further studies of the mechanism of bacteriorhodopsin functioning.

Fundus autofluorescence mostly originates from bisretinoid fluorophores in lipofuscin granules, which accumulate in retinal-pigment-epithelium cells with age. The dynamics of accumulation, photo-oxidation, and photodegradation of bisretinoids during aging or in the presence of pathology have been insufficiently investigated. Changes in spectral properties and composition of human lipofuscin-granule fluorophores with age and pathology have now been investigated by a high-performance liquid chromatography method using spectrophotometric and fluorescent detectors connected in series. It was found that: (i) N-retinylidene-N-retinylethanolamine (A2E) fluorescence intensity is not predominant in the chloroform extract of human-cadaver-eye retinal pigment epithelium studied; bisretinoid photo-oxidation and photodegradation products have much higher fluorescent properties; (ii) the relative emission maximum in the fluorescence spectrum of suspended retinal-pigment-epithelium cells obtained from an individual human-cadaver eye without pathology is irrespective of donor age and falls within the range 575 ± 15 nm; in two cadaver eyes with signs of age-related macular degeneration, emission maxima were shifted by 23-36 nm towards the shortwave region; and (iii) the ratio of bisretinoid photo-oxidation and photodegradation products to unoxidized bisretinoids in the chloroform extract of cadaver-eye retinal pigment epithelium increases with donor age, from 0.69 ± 0.03 to 1.32 ± 0.04. The differences in fluorescence properties between chloroform extracts obtained from cadaver eyes with and without signs of age-related macular degeneration could be used to increase the potential of fundus autofluorescence imaging as a noninvasive diagnostic method.

Ultrafast reverse photoreaction of visual pigment rhodopsin in the femtosecond time range at room temperature is demonstrated. Femtosecond two-pump probe experiments with a time resolution of 25 fs have been performed. The first pump pulse at 500 nm initiated cis-trans photoisomerization of rhodopsin chromophore, 11-cis retinal, which resulted in the formation of the primary ground-state photoproduct within a mere 200 fs. The second pump pulse at 620 nm with a varying delay of 200 to 3750 fs relative to the first pump pulse, initiated the reverse phototransition of the primary photoproduct to rhodopsin. The results of this photoconversion have been observed on the differential spectra obtained after the action of two pump pulses at a time delay of 100 ps. It was found that optical density decreased at 560 nm in the spectral region of bathorhodopsin absorption and increased at 480 nm, where rhodopsin absorbs. Rhodopsin photoswitching efficiency shows oscillations as a function of the time delay between two pump pulses. The quantum yield of reverse photoreaction initiated by the second pump pulse falls within the range 15% ± 1%. The molecular mechanism of the ultrafast reversible photoreaction of visual pigment rhodopsin may be used as a concept for the development of an ultrafast optical molecular switch.

The dynamics of the coherent photoisomerization of the 11-cis-retinal in bovine rhodopsin is studied by femtosecond time-resolved laser absorption spectroscopy with a resolution of 30 fs. Rhodopsin is excited with 500-, 535-, and 560-nm femtosecond pulses to produce different initial Franck-Condon states with different vibrational energies of the molecule in its electronically excited state. The time evolution of the photoinduced differential absorption spectra of rhodopsin is measured upon excitation with a femtosecond pulse in a spectral range from 400 to 720 nm. Oscillations in the time-resolved absorption of the rhodopsin photoproducts, such as photorhodopsin with a vibrationally excited all-trans-retinal and in its initial-state rhodopsin with a vibrationally excited 11-cis-retinal, are examined. It is demonstrated that these oscillations reflect the dynamics of coherent vibrational wavepackets. The Fourier transform of these oscillatory components yields frequencies, amplitudes, and initial phases of various vibrational modes involved in the motion the wavepackets in both photoproducts. The main vibrational modes manifest themselves at frequencies of 62 and 160 cm−1 for photorhodopsin and 44 and 142 cm−1 for initial-state rhodopsin. It is shown that these vibrational modes are directly involved in the coherent reaction under the study, with their amplitudes in the power spectrum produced by the Fourier transform of the kinetic curves being dependent on the wavelength of rhodopsin excitation.

The pharmacological properties and mechanisms of action of the flavanoid rutin were reviewed. Rutin can interact with free radicals and various protein systems to exhibit antioxidant, anti-inflammatory, anti-allergy, and antitumor activity. At present, much research is devoted to studies of the mechanisms of rutin pharmacological action.

Photochromic ultrafast reactions of bacteriorhodopsin ( H . salinarum ) and bovine rhodopsin were conducted with a femtosecond two-pump probe pulse setup with the time resolution of 20–25 fs. The dynamics of the forward and reverse photochemical reactions for both retinal-containing proteins was compared. It is demonstrated that when retinal-containing proteins are excited by femtosecond pulses, dynamics pattern of the vibrational coherent wave packets in the course of the reaction is different for bacteriorhodopsin and visual rhodopsin. As shown in these studies, the low-frequencies that form a wave packets experimentally observed in the dynamics of primary products formation as a result of retinal photoisomerization have different intensities and are clearer for bovine rhodopsin. Photo-reversible reactions for both retinal proteins were performed from the stage of the relatively stable photointermediates that appear within 3–5 ps after the light pulse impact. It is demonstrated that the efficiency of the reverse phototransition K -form → bacteriorhodopsin is almost five-fold higher than that of the Batho -intermediate → visual rhodopsin phototransition. The results obtained indicate that in the course of evolution the intramolecular mechanism of the chromophore-protein interaction in visual rhodopsin becomes more perfect and specific. The decrease in the probability of the reverse chromophore photoisomerization (all- trans → 11- cis retinal) in primary photo-induced rhodopsin products causes an increase in the efficiency of the photoreception process.

Lipofuscin granules accumulate in the cells of retinal pigment epithelium with age, particularly in patients with hereditary diseases. These granules are heterogeneous, being composed of mixtures of proteins and lipids, including more than 21 different fluorescent compounds. Bisretinoids and their photo-oxidation and photodegradation products represent the main source of lipofuscin fluorescence and exhibit phototoxic properties. This study used time-of-flight secondary ion mass spectrometry (ToF–SIMS) with in-depth probing to assess the depth distribution of N-retinylidene-N-retinylethanolamine (A2E) and its singly and doubly oxidized forms (A2E-ox and A2E-2ox, respectively) within lipofuscin granules and in their surface layer (lipid membrane). ToF–SIMS showed that A2E and its oxidized forms were uniformly distributed throughout lipofuscin granules but were not present at the membrane surface layer. This finding is important for understanding the process involved in the formation of lipofuscin granules and in their toxicity.

The review concerns literature data on the structure, functions and molecular simulation of rhodopsin. The mechanisms of the spectral tuning of visual pigments, photoisomerization of the rhodopsin chromophore group (11-cis-retinal moiety) and the formation of the physiologically active state of rhodopsin as a G-protein-coupled receptor are considered. Particular attention is given to the rhodopsin visual cycle and pathogenetic consequences of its impairment. A knowledge of the structure and photochemistry of rhodopsin was shown to be of importance for the use in nanotechnology of the future. The bibliography includes 219 references.

Saturation transfer EPR spectroscopy is used to study the photoinduced conformational changes of spin-labeled (Cys140 and Cys316) rhodopsin in a photoreceptor membrane. Illumination of rhodopsin with “yellow” light (λ > 450 nm), converting it from the dark form into metarhodopsin II, a physiologically active form, is accompanied by an increase in the mobility of the cytoplasmic loop (Cys140) and eighth alpha-helix (Cys316), whereas the subsequent illumination with “blue” light (λ < 445 nm), which converts metarhodopsin II into a mixture of inactive photoregenerated products, results in a decrease in the mobility. The restoration of the specific features of the photoinduced changes in the conformational mobility of the cytoplasmic loops of rhodopsin regenerated in the dark is demonstrated.

A family of structurally related protein toxins extracted from bacteria or plants have a similar mechanism of action, namely, blocking protein synthesis by ribosome inactivation. Members of this family of ribosome-inactivating proteins (RIP), classified simultaneously as chemical and biological threat agents, include ricin, abrin, and shiga toxins. We have adapted and streamlined mass spectrometry based functional assays, described by others, to develop a rapid, robust, broad-band and fieldable protocol with the primary goal of RIP toxin detection in unknown powder materials. Complementary to intact protein detection and proteomics methods, this protocol involves monitoring the depurination of selected DNA substrates by mass spectrometry. It is being implemented on the CB-TOF system for rapid detection of bio-threats by MALDI MS. Here we illustrate its performance on the example of a plant (ricin) and a bacterial (shiga) RIP toxin.

The content of carotenoids and retinoids was compared in the eyes of two Finnish populations of the opossum shrimp, Mysis relicta, which have been reproductively isolated for at least 9000 years: one from the deep, dark, Lake Paajarvi, the other from the Baltic Sea (Pojoviken Bay). The eyes of the lake population (LP) are highly susceptible to light damage, while those of the sea population (SP) are more resistant. Carotenoids are known to act as antioxidants protecting cells against free radicals and reactive oxygen species; retinoids, on the contrary, may be phototoxic in certain conditions. Analyzed by spectrophotometry and HPLC, the carotenoid content was broadly similar in the eyes of the two populations as regards both total amount and relative proportions of more than 20 components. Noteworthy differences were found in only three of the major components, among these astaxanthin, which was two times higher in SP compared with LP. The most interesting finding was the 1.6-fold higher content ...

Visible light-induced changes in fluorescence characteristics of lipofuscin granules (LG) isolated from retinal pigment epithelium of human cadaver eyes are compared with the analogous age-related changes and correlated with the content and photooxidation of LG main fluorophore, A2E. We used HPLC to examine changes of LG fluorophore composition with donor age, as well as before and after visible-light irradiation (the latter HPLC tests were also done with synthetic A2E). Visible light induces oxidation of LG fluorophores. As a result, their fluorescence characteristics change: the emission spectrum is blue-shifted by 25–40 nm. The observed age-dependent changes in the relative content of LG fluorophores and their oxidized derivatives were qualitatively similar with those caused by irradiation. To improve the accuracy of a new noninvasive diagnostic method, fundus autofluorescence imaging, it is important to know the ratio of nonoxidized and oxidized fluorophore derivatives depending on age and eye pathology.

The interaction of all-trans-retinal (hereinafter referred to as retinal) with planar bilayer lipid membranes has been studied. Addition of retinal into aqueous solutions on both sides of the membrane formed from diphytanoilphosphatidylcholine (DPhPC) or its mixture with diphytanoilphosphatidylethanolamine (DPhPC/DPhPE in w/w proportion of 3: 5) led to a change of conductance induced by ionophores nonactin (increase of conductance) or pentachlorophenol (decrease). Increase of nonactin-induced conductance was dependent on the membrane lipid composition and was two times higher in the case of DPhPC/DPhPE mixture. The change of conductance caused by ionophores of different signs (plus or minus) had different direction suggesting the influence of the retinal on the dipole potential upon its incorporation into BLM. The boundary potentials difference measured by the intramembrane field compensation method (IFC) after the retinal addition on one side of the membrane did not exceed 2.5 mV suggesting that its distribution in the bilayer is almost symmetrical. The illumination of the retinal-containing BLM caused a decrease in its lifetime when the membranes were formed from unsaturated lipids. Retinal incorporated into BLM led also to photoinactivation of the gramicidin channels. The process was completely inhibited by a singlet oxygen quencher (sodium azide). These results indicate that retinal accumulated in the membrane can affect both membrane proteins and the unsaturated lipids by their oxidation by the singlet oxygen.

We have reproduced the model system containing A2-rhodopsin, NR-PE, A2-PE, and ATR-dimer-PE in order to study photosensitized damage of rhodopsin within photoreceptor membranes of rod outer segments. We have demonstrated that irradiation of such a system with visible light (400-700 nm) distorts the most important functional property of native visual pigment--its ability to regenerate after addition of 11-cis-retinal in the dark. We have also shown that all-trans-retinal bound to membrane phospholipids and rhodopsin has less photosensitizing activity that free all-trans-retinal.

Carotenoids were found for the first time in the vitreous body of human eye during the fetal period from week 15 until week 28. Their maximum content was timed to week 16–22. No carotenoids were found the vitreous body of 31-week fetuses, as well as adult humans, which corresponds to the published data. It was shown using HPLC that chromatographic characteristics of these carotenoids correspond to those of lutein and zeaxanthin, characteristic pigments of the retinal yellow macula.

Supramolecular organization of rhodopsin in the photoreceptor membrane was investigated by small-angle neutron scattering method. The experiments, which were performed with mixtures of heavy/light water as solvent (contrast variation method), were aimed at obtaining information about the lipid and protein components of the photoreceptor disc membrane separately. It was shown that the packaging density of the rhodopsin molecules in the photoreceptor membrane was unusually high: the distance between the centers of the molecules was approximately 56 A. The probability of the monomeric state of rhodopsin molecules in the photoreceptor membrane, according to the data obtained, is rather high.

Human noroviruses (HuNoVs) are positive-sense RNA viruses that can cause severe, highly infectious gastroenteritis. HuNoV outbreaks are frequently associated with recombination between circulating strains. Strain genotyping and phylogenetic analyses show that noroviruses often recombine in a highly conserved region near the junction of the viral polyprotein (open reading frame 1 [ORF1]) and capsid (ORF2) genes and occasionally within the RNA-dependent RNA polymerase (RdRP) gene. Although genotyping methods are useful for tracking changes in circulating viral populations, they report only the dominant recombinant strains and do not elucidate the frequency or range of recombination events. Furthermore, the relatively low frequency of recombination in RNA viruses has limited studies to cell culture or in vitro systems, which do not reflect the complexities and selective pressures present in an infected organism. Using two murine norovirus (MNV) strains to model coinfection, we developed a microfluidic platform to amplify, detect, and recover individual recombinants following in vitro and in vivo coinfection. One-step reverse transcriptase PCR (RT-PCR) was performed in picoliter drops with primers that identified the wild-type and recombinant progenies and scanned for recombination breakpoints at ∼1-kb intervals. We detected recombination between MNV strains at multiple loci spanning the viral protease, RdRP, and capsid ORFs and isolated individual recombinant RNA genomes that were present at a frequency of 1/300,000 or higher. This study is the first to examine norovirus recombination following coinfection of an animal and suggests that the exchange of RNA among viral genomes in an infected host occurs in multiple locations and is an important driver of genetic diversity. IMPORTANCE RNA viruses increase diversity and escape host immune barriers by genomic recombination. Studies using a number of viral systems indicate that recombination occurs via template switching by the virus-encoded RNA-dependent RNA polymerase (RdRP). However, factors that govern the frequency and positions of recombination in an infected organism remain largely unknown. This work leverages advances in the applied physics of drop-based microfluidics to isolate and sequence rare recombinants arising from the coinfection of mice with two distinct strains of murine norovirus. This study is the first to detect and analyze norovirus recombination in an animal model.

Ribavirin is a pharmaceutical antiviral used for the treatment of RNA virus infections including norovirus, hepatitis C virus, hepatitis E virus, Lassa virus, respiratory syncytial virus, and rhinovirus. Despite the drug's history and documented efficacy, the antiviral mechanism of Ribavirin remains unclear. Mechanisms proposed include depletion of the intracellular GTP pool, immunomodulatory effects, induction of error catastrophe, inhibition of viral polymerase activity, and/or inhibition of viral capping. In the present study, we leveraged deep sequencing data to demonstrate that Ribavirin increases murine norovirus (MNV-1) viral diversity. By serial passaging MNV-1 in RAW 264.7 cells for twenty generations in the presence of Ribavirin, we demonstrated statistically significant increases in both the number of unique haplotypes and the average pairwise difference (APD). Based on statistically significant differences in the probability of nucleotide mutations based on Roche 454 sequencing, we also demonstrated that single nucleotide substitutions are increased in the presence of Ribavirin. Finally, we demonstrated Ribavirin's impact on statistically significantly reducing the relative proportion of the dominant sequence within the quasispecies.

Plasmacytoid dendritic cells (PDC) are the natural type I IFN-producing cells that produce large amounts of IFN-α in response to viral stimulation. During attempts to isolate PDC from human PBMC, we observed that cross-linking a variety of cell surface receptors, including blood DC Ag (BDCA)-2, BDCA-4, CD4, or CD123 with Abs and immunobeads on PDC leads to inhibition of IFN-α production in response to HSV. To understand the mechanisms involved, a number of parameters were investigated. Cross-linking did not inhibit endocytosis of soluble Ag by PDC. Flow cytometry for annexin V and activated caspase-3 indicated that PDC are not undergoing apoptosis after receptor cross-linking. Cross-linking of CD123, but not the other receptors, caused the up-regulation of costimulatory molecules CD80 and CD86, as well as the down-regulation of CD62L, indicating PDC maturation. Thus, anti-CD123 Ab may be acting similar to the natural ligand, IL-3. Anti-phosphotyrosine Ab, as well as Ab to the IFN regulatory factor, IRF-7, was used in intracellular flow cytometry to elucidate the signaling pathways involved. Tyrosine phosphorylation occurred after cross-linking BDCA-2 and BDCA-4, but not CD4. Cross-linking did not affect IRF-7 levels in PDC, however, cross-linking BDCA-2, BDCA-4, and CD4, but not CD123, inhibited the ability of IRF-7 to translocate to the nucleus. Taken together, these results suggest that cross-linking BDCA-2, BDCA-4, and CD4 on PDC regulates IFN-α production at the level of IRF-7, while the decrease in IFN-α production after CD123 cross-linking is due to stimulation of the IL-3R and induction of PDC maturation.

Based on a computer molecular simulation, we have investigated the conformational dynamics of rhodopsin and its free opsin. A special emphasis was made on the behaviour of the chromophore group – 11- cis -retinal within the rhodopsin molecule in its dark-adapted state. The molecular dynamics trajectories were traced in the time range of 3000 ps. We have generated 3×10 6 discrete states of free opsin and rhodopsin in order to compare the rhodopsin and opsin structural conformation changes. Analysis of the 11- cis -retinal adjustment process in the chromophore site of opsin in correlation with the behaviour of the nearest surrounding amino acid residues has been carried out. The possible molecular mechanisms of the conformational adaptation of 11- cis -retinal in the protein binding pocket, which occur during the physiological regeneration of the visual pigment rhodopsin, are discussed.

This guide was compiled after recommendations by the American Institute for Cancer Research (AICR) Cancer Resource Advisory Council. It encompasses the AICR position on current issues in nutrition for cancer survivors during treatment and is intended to provide advice about dietary supplements for cancer survivors who are still being treated. Current scientific findings about the safety and effectiveness of some commonly used dietary antioxidants and nonantioxidant supplements during chemotherapy are presented and assessed. Use of dietary supplements during cancer treatment remains controversial. Patients are cautioned that vitamin and mineral supplements as therapies are not substitutes for established medicine. The current recommendation for cancer patients is to only take moderate doses of supplements because evidence from human clinical studies that confirm their safety and benefits is limited. A daily multivitamin containing supplements at the levels of the Dietary Reference Intakes can be used safely as part of a program of healthy nutrition. In addition, the AICR Cancer Resource Advisory Council concluded that further scientific research is needed to provide a set of firm guidelines for the use of vitamin and mineral supplements by cancer patients during treatment.

A novel method for acquisition and numerical analysis of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectral data is described. The digitized ion current transient from each consecutive laser shot is first acquired and stored independently. Subsequently, statistical correlation parameters between all stored transients are computed. We illustrate the uses of this event-by-event analysis method for studies of sample surface heterogeneity as well as for elucidating the mechanisms of ion formation in MALDI. Other potential applications of the method are also outlined.

The author and four independent experts evaluated the intent and quality of scientific evidence for a potential beneficial health relationship between the intake of walnuts and the reduction and prevention of coronary heart disease. The report also addresses the supporting evidence for the health benefit of other tree nuts and selected legumes. Compared to most other nuts, which contain monounsaturated fatty acids, walnuts are unique because they are rich in n-6 (linoleate) and n-3 (linolenate) polyunsaturated fatty acids. Walnuts contain multiple health-beneficial components, such as having a low lysine:arginine ratio and high levels of arginine, folate, fiber, tannins, and polyphenols. Though walnuts are energy rich, clinical dietary intervention studies show that walnut consumption does not cause a net gain in body weight when eaten as a replacement food. Five controlled, peer-reviewed, human clinical walnut intervention trials, involving approximately 200 subjects representative of the 51% of the adult population in the United States at risk of coronary heart disease were reviewed. The intervention trials consistently demonstrated walnuts as part of a heart-healthy diet, lower blood cholesterol concentrations. None of these studies were of extended duration that would be essential for evaluation of the sustainability of the observed outcomes. These results were supported by several large prospective observational studies in humans, all demonstrating a dose response-related inverse association of the relative risk of coronary heart disease with the frequent daily consumption of small amounts of nuts, including walnuts.

Drug use poses multiple challenges to maintaining physical health among HIV-infected individuals, particularly with regard to disease progression. Few studies, however, have examined the association between the use of crystal methamphetamine ("crystal meth") and HIV disease progression specifically among HIV-infected men who have sex with men (MSM). Understanding this relationship among HIV-infected MSM is particularly critical because of the high rates of crystal meth use reported in the population.Associations between recent crystal meth use and poor HIV medical outcomes (viral load200 copies/mL, CD4 count350 cells/mm(3)) were analyzed for 2896 HIV-infected MSM enrolled in Ryan White Part A programs in the greater New York metropolitan area between November 2010 and June 2012.Crystal meth use (reported by 4%) was independently associated with unsuppressed viral load (AOR=1.8, CI=1.1-2.9) in multivariate analyses controlling for sociodemographic characteristics. There was no significant relationship between crystal meth use and low CD4 counts.To date, little research has examined how crystal meth use influences HIV medical outcomes among HIV-infected MSM. This analysis showed a significant independent association between crystal meth use and unsuppressed viral load among MSM in an HIV service population. Future studies should examine biological and psychosocial mediators, moderators and confounders of this relationship to inform intervention development for MSM crystal meth users in HIV care settings.

Grapefruit juice enhances the effect of some commonly used medications by increasing their bioavailability via the selective down-regulation of a specific subfamily of the cytochrome P450 enzyme system in the small intestine.

Purpose: The authors describe the clinical feature of ten patients with a new syndrome characterized by the presence of retinal vasculitis, multiple macroaneurysms, neuro-retinitis, and peripheral capillary nonperfusion. Methods: The authors evaluated ten patients identified to have clinical features compatible with the syndrome of idiopathic retinal vasculitis, aneurysms and neuroretinitis (IRVAN). Clinical examination findings, sequential fundus photographs (when available), fluorescein angiograms, systemic investigations, response to therapy, and visual outcomes were reviewed. Results: Seven eyes of four patients sustained a marked decrease in visual acuity of 20/200 or worse. Visual loss was due to a combination of an exudative maculopathy and sequelae of retinal ischemia. Capillary nonperfusion was seen in all ten patients and was severe enough to warrant panretinal laser photocoagulation in six patients. Systemic investigations were uniformly noncontributory. Oral prednisone appears to have little beneficial effects on patients with this disorder. Conclusions: Patients with IRVAN have characteristic retinal features that readily identify this syndrome. An increased awareness of this rare syndrome may help to identify sight-threatening complications at an earlier stage. The authors caution against extensive medical investigations. Ophthalmology 1995;102:1089-1097