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At least 19 recordsLinked to original sources

PubMed1976

Light peak to dark trough ratio in clinical electro-oculography: influence of dark oscillations on the following light peak.

In the clinical standard EOG procedure the light rise potential is influenced by the preceding dark troughs oscillation. This is apparent in the different configuration of the light rise potential when following a dark trough instead of a steady state. Uninfluenced responses can be obtained only under steady-state conditions. Recording of the light peak potential in this manner may be used on a trial basis for clinical routine examination. Experimental and more detailed clinical studies require separate recording of light peak and dark trough potential, each preceded by a steady state. The evaluation of these responses, expressing them in percent of the steady state, should reveal more information than can be expected from the standard light peak to dark trough ratio.

Adult↗

PubMed2026

ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.

MOTIVATION: The accelerating crisis of antimicrobial resistance among the critical so-called ESKAPE pathogens demands the urgent identification of novel molecular targets. However, a substantial fraction of ESKAPE proteomes remains functionally uncharacterized, with many genes annotated as encoding hypothetical proteins. These protein sequences often lack significant similarity to known protein families when conventional homology-based annotation methods are used and thus remain "dark". This limits our ability to explore their roles in pathogenicity, and it is thus crucial to bridge this substantial gap in pathogen biology by developing new strategies to illuminate these "dark" regions of the ESKAPE pan-proteome. RESULTS: We introduce ECLIPSE (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration), a network-based computational framework that systematically identifies and prioritizes functionally dark protein families in ESKAPE pan-proteomes. ECLIPSE embeds target ESKAPE pathogen proteomes within the global sequence similarity network of the Protein Universe Atlas. It detects connected components composed entirely of unannotated proteins, called the "dark proteome." As a case study, we applied ECLIPSE to a pan-proteome of 3 460 657 protein sequences from 635 strains of Pseudomonas aeruginosa (PA). ECLIPSE identified 120 985 proteins (4%) residing in completely dark connected components. Furthermore, we have performed a taxonomic diversity analysis using normalized Shannon indices to characterize each dark component by its enrichment in ESKAPE pathogens. The analysis utilized the evenness (E) value (see Methods 2.1), which distinguishes Pseudomonas-specific (target-specific) from ESKAPE-enriched dark components. We then developed the Dark Proteome Prioritization Score (DPPS), a composite multidimensional scoring framework (see Methods 2.5). It ranks these dark components by biological relevance across four orthogonal axes: (i) functional darkness, (ii) P. aeruginosa proportion in the Atlas, (iii) AMR-clade taxonomic restriction, and (iv) conservation across the 635 P. aeruginosa strains. This framework outputs a robust four-tier scoring system; the prioritized Tier I components were validated by weight sensitivity analysis and remained stable across 500 Monte Carlo weight perturbations. Structural characterization of one of the top-ranked ESKAPE-enriched dark components revealed that it belongs to the beta-barrel fold DUF1302 (PF06980) family, for which no experimentally solved three-dimensional structure exists in the PDB. The genomic context analysis indicates that it is co-localized with a LuxR-type transcriptional regulator. Collectively, ECLIPSE identifies evolutionarily conserved, structurally defined, and functionally dark proteins enriched across ESKAPE pathogens; these dark proteins can further be utilized as alternative antimicrobial targets for experimental characterization. AVAILABILITY AND IMPLEMENTATION: The source code and dataset are available for free at: Github: https://github.com/surabhilata/ECLIPSE.git, Zenodo: DOI: 10.5281/zenodo.21064323.

Proteome↗

PubMed1977

Dark adaptation in diabetics.

Dark adaptation in diabetics was recorded with Goldmann-Weeker's adaptometer and analysed according to the stages of retinopathy by Scott. Dark adaptation curves in diabetics were divided into three groups; normal dark adaptation; subnormal one which showed normal first curve of dark adaptation and impaired second curve; abnormal dark adaptation which showed impaired dark adaptation in the whole course. The cases with normal dark adaptation were found to be few in the stages Ia, II and IIIa of retinopathy. Subnormal dark adaptation was rarely found in the stages Ia, II, IIIa and IIb of retinopathy. Abnormal dark adaptation was recorded in most patients with diabetic retinopathy and found in all th stages of retinopathy. A 5% level of significance was statistically recognized in the thresh old at 35 min after light adaptation between the stages IIIa and IIIb of retinopathy. From this viewpoint, significance in severity of diabetic retinopathy was discussed.

Dark Adaptation↗

PubMed1976

Effects of continuous light and darkness on the eyes of the troglobitic salamander Typhlotriton spelaeus.

Larval Typhlotriton spelaeus collected from five caves in Pulaski Co., Missouri, were kept as larvae or induced to transform in darkness or continuous fluorescent illumination. Larvae maintained in darkness for 215 and 279 days had smaller eyes, smaller rod inner and outer segments, and fewer metaphase figures in the germinative zone of the neural retina than comparable larvae maintained in light (258 lux). Except for visual cell size, differences were small and for each characteristic exceptions were observed. One larva kept in light showed early retinal degeneration comparable to that in transformed adults to T. spelaeus. All larvae exhibited optomotor behavior both before and after the experiment. Among animals induced to transform by L-thyroxin and maintained in darkness 111 to 366 days, visual cell and pigment epithelium degeneration was more extensive and more frequent than in animals kept for the same length of time in light (237-298 lux). In darkness the frequency of animals with retinal degeneration increased between 111 and 366 days. In light some animals exhibited pigment epithelium reduction with normal visual cells, and others had free, pigmented cells in the subretinal space. These effects were not comparable to degeneration in darkness. Eyelids covered the eyes of only a few animals in both light and dark treatments. The extent of eyelid encroachment over the eye greater in darkness than in light. Most animals exhibited optomotor responses after experiments, but responses of animals kept in darkness were impaired in comparison to those of animals kept in light.

Animals↗

PubMed1975

Light-sensitive swelling of isolated frog rod outer segments as an in vitro assay for visual transduction and dark adaptation.

Frog rod outer segments swell slowly after being shaken from an excised retina into a modified Ringer's solution. The swelling has the following characteristics: (a) It is suppressed by illumination which bleaches only 500 rhodopsin molecules per outer segment per second. This is approximately the level required to saturate the in vivo receptor potential. (b) Light suppression is seen in NaCl but not in KCl solutions. (c) Dark swelling is labile and is enhanced by calf serum, low calcium concentrations, dithiothreitol, and cyclic nucleotide phosphodiesterase inhibitors. (d) Lowering the pH to 5.5 or removing magnesium reversibly reduces dark swelling to the same extent as illumination. (e) The amount of light required for maximal suppression of dark-swelling increases approximately 10-fold if the calcium concentrations is lowered by EGTA addition. (f) The effect of illumination is irreversibly abolished by antimycin and other inhibitors of mitochondrial electron transport. (g) A process analogous to dark adaptation in vivo can be observed: If 10-50% of the rhodopsin present is bleached and the outer segments are then kept dark, rapid dark swelling returns after a period of 15-45 min. This swelling is again sensitive to light. We tentatively ascribe the light suppression of swelling to the same decrease in sodium permeability which is observed on illuminating living receptor cells. The experiments suggest that outer segments retain their competence to perform both transduction and dark adaptation after their separation from the retina.

Animals↗

PubMed1978

Dark-adaptation in abnormal (RCS) rats studied electroretinographically.

1. Electroretinogram (e.r.g.) responses recorded from dark-reared rats with inherited retinal dystrophy (RCS) showed progressive decline in b-wave ampliture and prolongation of the time to the peak of the b-wave with age when compared with records obtained from dark-reared normal albino rats. 2. Dark-adaptation was followed in RCS and normal rats by recording the light intensity needed to evoke a criterion e.r.g. response at different time intervals after bleaching and 90% of the rhodopsin. 3. In normal rats, dark-adaptation was governed by two mechanisms. The first 25--35 min of recovery was determined by cones. The second branch, determined by the recovery of rods, lasted for about 3 hr and proceeded along an exponential time course with time constant of 41.4 +/- 2.4 min (S.E. of mean). 4. In RCS rats, the time course of the dark-adaptation after a 90% bleach depended on age. In 25--30 day old rats the recovery curve had at least three breaks separating three different mechanisms. Rats, 35--40 days old, exhibited double exponential recovery curves, while 45--70 day old rats recovered along a single exponential curve similar in time course to the cone branch of dark-adaptation found in normal rats. 5. Action spectra obtained from RCS rats at different time intervals of the recovery curve showed that in young rats, 25--30 days old, small e.r.g. responses recorded before bleaching and at the end of the recovery period were determined by rhodopsin while those recorded during the first part of the recovery from 90% bleach were determined by a combination of rods and cones. In RCS rats of advanced age (45--70 days old), rhodopsin was the major contributor to the e.r.g. responses recorded either before bleaching or at the end of the recovery period. 6. The gradual deterioration with age of the e.r.g. in RCS rats cannot be explained by either the decrease in quantum catch due to the decrease in rhodopsin content or by the linear relationship between log e.r.g. threshold and pigment concentration. 7. Using estimates of rhodopsin density within surviving rods obtained from retinal densitometry, it was shown that in RCS rats where more than 30% of normal levels of rhodopsin was located within the functioning rods, the log intensity needed for a criterion e.r.g. response measured at the end of the recovery period from a 90% bleach was linearly related to the fraction of 'functional' rhodopsin. 8. No simple relationship between log e.r.g. threshold and rhodopsin concentration could be found during the course of recovery in the dark from a strong bleaching exposure in RCS rats of all ages.

Age Factors↗

PubMed1979

The localisation of lead in the skin of light- and dark-adapted Xenopus laevis.

Toads pretreated for 2 months on either a dark or a light background were then exposed to lead nitrate at 50 ppm lead for 21 days, the illumination regimes being maintained. Metal analysis of dorsal skin showed significantly higher lead levels (p less than 0.01) in dark-adapted toads. No precipitated lead deposits were observed at the ultrastructural level, necessitating X-ray microanalysis of sections containing melanophores, gland cells and general (non-melanophore) cytoplasm. Analysis showed the lead to be concentrated within the melanosomes of the melanophores, and to be significantly higher (p less than 0.01) in individual melanosomes of dark-adapted toads than in light adapted ones. Copper was also found to be concentrated in the melanosomes and was higher (p less than 0.01) in the melanosomes of the dark-adapted toads. The results are consistent with the known affinity of melanin for heavy metals and the documented increase in melanophore number under prolonged dark background regimes. Since all toads received the same lead exposure, the melanosome results give rise to speculation that higher melanin levels might occur in individual melanosomes of dark-adapted skin.

Adaptation, Physiological↗

PubMed1975

Application of visually evoked response near the threshold of vision to objective measurement of dark adaptation.

The visually evoked response (VER) to dim lights with intensities within the scotopic or lower mesopic range increased in amplitude during the progressive dark adaptation. The VER amplitude vs. time curve resembled the psychophysical dark adaptation curve. The spectral sensitivity curve of the dark-adapted VER matched the C.I.E. scotopic sensitivity curve. The dark-adapted VER was abnormal in patients with retinitis pigmentosa and with congenital stationary night blindness and recordable in a patient with cone dysfunction. There was a close correlation between the VER threshold and subjective threshold of visual perception. The dark-adapted VER may be useful as an objective index of dark adaptation.

Adaptation, Ocular↗

PubMed1978

Determination and modification of the redox state of the secondary acceptor of photosystem II in the dark.

The redox state of the secondary electron acceptor B of Photosystem II was studied using flourescence measurements. Preillumination of algae or chloroplasts with a variable number of short saturating flashes followed rapidly by the addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea induces oscillations of the initial level of fluorescence. The phase of these oscillations is characteristic of a given B/B-ratio in the dark-adapted samples. We conclude from our results that about 50% of the secondary electron acceptors are singly reduced in the dark in chlorella cells, but that more than 70% are fully oxidized in the dark adapted chloroplasts. Benzoquinone treatment modifies this distribution in Clorella leading to the same situation as in chloroplasts, i.e. more than 70% of the secondary acceptors are oxidized in the dark. The same ratio is observed if these algae are illuminated and then dark-adapted, unless an artificial donor (hydroxylamine) is added before this illumination. In that case about 50% B- is generated and stabilized in the dark.

Chlorella↗

PubMed1976

Sleep and motor activity of the rat during ultra-short light-dark cycles.

The vigilance states and motor activity of the rat were recorded during ultrashort light-dark (LD) cycles. The LD schedules were the following: 10 min light -- 10 min dark (LD 10:10), LD 7.5:7.5, LD 5:5 and LD 2.5:2.5. With all short LD schedules, paradoxical sleep (PS) and high motor activity occurred more frequently during dark periods than during light. PS and motor activity were rapidly enhanced by darkness and inhibited by light, whereas the percentages of total sleep and slow wave sleep were only gradually decreased during the dark periods and increased during light. Compared to the LD 12h:12h control days, sleep was enhanced by all short LD schedules, an effect that was most marked in the circadian phase of maximum waking (corresponding to the LD 12h:12h dark period). The short LD cycles interacted with an intrinsic sleep cycle, whose period is approximately 10 min. Interval histograms of PS episodes showed that an optimal synchronization of the ultradian sleep rhythm is achieved when the period of the LD cycle or its multiple correspond also to 10 min. It is suggested that the response of PS and motor activity to changes in illumination may be due to common mechanisms.

Animals↗

PubMed1979

Scotophobin A causes dark avoidance in goldfish by elevating pineal N-acetylserotonin.

We had shown that synthetic rat scotophobin A caused several effects upon goldfish, apparently mediated by the pineal gland. Here we report that norepinephrine decreased goldfish dark avoidance in a manner that was blocked by scotophobin or pinealectomy. Increased dark avoidance was caused by either propranolol or scotophobin alone. Certain components of the pineal melatonin pathway also affected goldfish light-dark preference: serotonin, and especially N-acetylserotonin, increased dark avoidance, as did the hydroxyindole-O-methyl-transferase (HIOMT) product inhibitor, S-adenosyl-homocysteine. Melatonin and S-adenosyl-methionine were without effect in this regard. Pinealectomy prevented the dark avoidance increase caused by serotonin and N-acetylserotonin. These data suggested that increased dark avoidance behavior in goldfish was correlated with N-acetylserotonin buildup in the pineal, and that scotophobin could cause this, if it were to inhibit pineal HIOMT. To test this hypothesis the effect of various agents upon pineal melatonin levels was determined. Scotophobin was found to both reduce pineal melatonin and to block the melatonin-increasing effect of N-acetylserotonin. This led to the discovery that, indeed, scotophobin was an effective inhibitor (KI50, 6 x 10(-7) M) of purified bovine HIOMT.

Acetylserotonin O-Methyltransferase↗

PubMed1979

Dark-adaptation of the aspartate-isolated rod receptor potential of the frog retina: threshold measurements.

1. The dark-adaptation of the aspartate-isolated rod receptor potential of the isolated and perfused frog retina has been measured after bleaching about 5-10% of the rhodopsin. The fraction bleached (DeltaR) and the decay of rhodopsin photoproducts were determined using alternating measurements with a photometric technique (Donner & Hemilä, 1975).2. The dark-adaptation time course of the log threshold elevation is exponential, log I(t)/I(0) = W exp (-t/tau)+P, where W is the extrapolated value for log I(t)/I(0)-P at t = 0 and P is log I(t)/I(0) for t = infinity. When DeltaR increases from 2 to 10% W increases from ca. 2.6 to ca. 5. The time constant tau is about 13 min at 9 degrees C and 7 min at 14 degrees C (DeltaR = 5-10%).3. When the bleaching period is extended, keeping the amount bleached (Ixt) constant, dark-adaptation is completed earlier.4. The time course of dark-adaptation and the decay of the photoproduct ;retinal' are similar, as is also their dependence on temperature (Q(10) approximately 3).5. The permanent log threshold rise P is approximately proportional to DeltaR after small bleaches; when more than about 10% is bleached the slope of the curve P(DeltaR) decreases. P is considerably larger (about 2.5-fold) for the same fraction bleached in experiments at 14 degrees C as compared to experiments at 9 degrees C.6. A comparison with previously obtained corresponding values for dark-adaptation after small bleaches at the ganglion cell level shows a close agreement between the time constants for the dark-adaptation curve, its range and the dependence of threshold on the fraction of rhodopsin bleached.

Animals↗

PubMed1979

A darkness induced eye abnormality in the domestic chicken.

Two-hundred broiler-type chickens were reared under either normal lighting or darkness for 16 weeks. Each week, birds were subjected to applanation tonometry for measurement of intraocular pressures (IOP). The birds were then weighed, eye enucleated, and dimensions measured. All eyes were prepared for histological examination. Chickens reared in darkness for 4 to 6 weeks displayed an abnormal eye enlargement, accompanied by an increase in IOP in comparison to chickens reared under conventional management. From the 6th to the 16th week, the eyes of dark-reared chickens continued to enlarge while IOP decreased. The sclera, choroid, retina, and retinal layers of dark-reared chicks were not as thick as controls throughout the 16 weeks. Two principle retinal pathologies were induced by darkness. One appeared as darkened areas of the peripheral retina. In histological sections the darkened retinal areas had a thin choroid and thin retinal layers. The second retinal abnormality was one or more white, nonpigmented bands directed perpendicular to the pectin. Histologically, the depigmented bands were areas in which the vessels of the choroid, the pigmented epithelium, and the outer retinal layers were absent. The corneas of dark-reared chicks exhibited a reduction in their curvature and thickness compared to control corneas.

Aging↗

PubMed1978

The effects of dark rearing on the development of the visual cortex of the rat.

The effects of dark rearing on the development of the visual cortex has been studied in Wistar rats, as have the effects of subsequent light exposure on recovery. Five groups of animals were used: (1) light exposed until 30-40 days post partum (dpp) (2) dark reared until 30-40 ddp (3) dark reared until 80-120 dpp (4) dark reared to 21 dpp, then light exposed until 40 dpp (5) light exposed to 21 dpp and then dark reared until 40 dpp. Golgi-Cox impregnations of layer IV stellate cell dendritic fields were analysed and total neuronal and glial counts were also done within layer IV of the primary visual cortex. Normal visual stellate cell dendritic fields were radially organised, with the highest dendritic density being recorded below the soma. In short term visually deprived animals and in the exposed only for 21 dpp and then reared in light until 40 dpp the radial distribution of dendrites was maintained but the peak density shifted to above the soma. In all other experimental groups this abnormal polarisation was still present but not as marked. Measurement of branching indices suggested that these field changes resulted from increased branching and growth in the superficial domain and not from the reorientation of dendrites. Differential glial counts revealed a significantly higher number of microglia in dark reared animals than in controls. Neuronal numbers were not affected.

Animals↗

PubMed1979

Effects of the duration of dark rearing on visually guided behavior in the kitten.

Forty-eight kittens were dark reared or light reared from birth for 1 to 8 months and formed 6 age groups. Following rearing the kittens were examined daily in several tasks of visually guided behavior. Compared to younger dark-reared groups of kittens, older deprived groups showed longer acquisition times for visual placing to a surface, visual tracking, visually guided reaching to a serrated edge and moving object, and visually guided locomotion on elevated platforms. After dark rearing durations of 3 months or longer, deprived groups displayed overall deficiencies in obstacle avoidance during their 1st postdeprivation month. The older dark-reared groups gave some indication of a direct relationship between duration of dark rearing and both delay in acquisition times for the visually guided behaviors and deficiency in obstacle avoidance. One interpretation of the results is that during dark rearing the kitten may acquire nonvisual behaviors which could interfere with and prolong its development of visually guided behavior subsequent to deprivation.

Animals↗

PubMed1977

Dark adaptation and receptive field organisation of cells in the cat lateral geniculate nucleus.

The receptive fields of LGN cells were investigated with stationary light and dark spot and annulus stimuli. Stimulus size and background intensity were varied while stimulus/background contrast was kept constant. The speed of dark adaptation vaired considerably from cell to cell. Dark adaptation made responses more sustained in all neurones and eliminated the oscillatory on-responses evoked under some conditions in the light-adapted cells. Dark adaptation led also to a disappearance of early phasic inhibition in on-responses, and increased response rise time and latency. The power of surround responses to inhibit centre responses decreased slightly at low levels of light adaptation in LGN cells but much less than in retinal ganglion cells. Some other traces of changing retinal surround effects also appeared inthe LGN on dark adaptation. For example, the functional size of receptive fields increased at low levels of illuminance as has been observed in retinal ganglion cells and the receptive fields as estimated from response peaks were larger than those estimated from sustained components.

Animals↗

PubMed1976

Light-dependent development of thermoluminescence, delayed emission and fluorescence variation in dark-grown spruce leaves.

Thermoluminescence profiles of spruce leaves grown under various light or dark conditions were measured after excitation at a low temperature (-70 to -20 degrees C) by 1-min illumination with red light, and the following results were obtained. Mature spruce leaves showed five thermoluminescence bands at -30, -5, +20, +40 (or +35) and +70 degrees C (denoted as Zv, A, B1, B2 and C bands, respectively), but dark-grown spruce leaves with a similar chlorophyll content showed only two bands, at -30 and +70 degrees C (the Zv and C bands) and were devoid of the three other bands (the A, B1, and B2 bands). On exposure of the dark-grown leaves to continuous red light, the A, B1and B2 bands were rapidly developed, and the development was accompanied by enhancement of delayed emission, fluorescence variation and the Hill activity (photoreduction of 2,6-dichlorophenolindophenol with water as electron donor). It was demonstrated that the dark-grown spruce leaves are devoid of the water-splitting system in Photosystem II, and that the latent water-splitting activity is rapidly photoactivated by exposure of the leaves to continuous red light. These results on the gymnosperm spruce leaves, in which greening proceeds in complete darkness, being independent of the development of the water-splitting system in light, were discussed in relation to previous observations on angiosperm leaves, in which both greening and the activity generation proceed in the light.

Chlorophyll↗

PubMed1978

"Dark-active" rat transformed into "light-active" rat by destruction of 24-hr clock: function of 24-hr clock and synchronizers.

In alternating 12-hr periods of light and dark the rat is active mainly in the dark. Its activity in the dark (beginning at 1800) depends exclusively on release of activity by the 24-hr clock. In the light (beginning at 0600) the 24-hr clock inhibits activity; the normal rat becomes totally inactive in the light except for activity resulting from external stimulation. After section of the connections between the optic chiasma and the hypothalamus, some rats become totally and permanently inactive in the dark. This sectioning destroys the 24-hr clock. After destruction of the clock removes inhibition of activity in the light period, the rat becomes active promptly at start of the light period--i.e., becomes a "light-active" animal. In the normal rat, activity becomes synchronized to start of the dark (by the electric clock at 1800), regardless of the amounts of activity. Destruction of the 24-hr clock eliminates the synchronizer at 1800. However, almost at once, activity, eating, and drinking are kept together by a second synchronizer, start of the light (by the electric clock at 0600). This may explain the ability of the rat to survive after destruction of the 24-hr clock.

Animals↗