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At least 19 recordsLinked to original sources
PubMed1992

'Dark' cell formation under protein malnutrition: process of conversion and concept of 'semi-dark' type Purkinje cells.

This paper deals with some deleterious effects of protein malnourishment in rat cerebellum. Severe protein deprivation enhanced the formation of 'dark' cells in white rats. It is postulated that abnormal changes in the neuronal contents induced by nutritional stress play a vital role in the formation of the 'dark' cells through an intermediary stage, 'semi-dark' cells. Centrophenoxine a lipofuscinolytic agent, however, seems to interfere with the process of formation of 'dark' cells and/or helps reconversion of the 'dark' cells into the normal or 'light' type Purkinje cells.

Animals↗
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↗
PubMed1991

Rapid reentrainment of the circadian clock itself, but not the measurable activity rhythms to a new light-dark cycle in the rat.

Experiments were performed to determine if the circadian clock reentrains more quickly to an 8-hour phase shift in light-dark (LD) cycles than does the overt rhythm of activity. To investigate the reentrainment of the clock itself to an 8-hour advance or delay in the LD cycle, the rats were released into constant darkness only two or three days after a shift in LD cycle, and the amount of the phase shift of the clock itself was estimated from where free-running rhythm started by backward extrapolation. If the circadian clock could rapidly reset itself to the new LD cycle, it was predicted that the free-running rhythm of activity would start from near the dark period of the new LD cycle rather than the preceding one. When rats were released into constant darkness three days after the LD cycle was advanced by 8 hours, the activity of the free-running rhythm started near time of dark period of the new LD cycle in all rats (n = 16). When rats (n = 24) were released into constant darkness two days after the LD cycle was advanced by 8 hours, 12 rats started the activity near time of dark period of the new LD cycle, while 9 rats started the activity near time of dark period of the preceding LD cycle. The remaining 3 rats showed the activity of the free-running rhythm near intermediate phase (transient phase). On the other hand, when the rats were not released into constant darkness after LD cycle was advanced by 8 hours, it took 6.4 days for activity rhythm to reentrain to the advanced LD cycle.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
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↗
PubMed1991

Comparison of serotonin 5-HT1 receptors and innervation in the visual cortex of normal and dark-reared cats.

The visual cortical serotoninergic system was compared in normal and dark-reared cats to determine whether visual experience is necessary for its normal development. In vitro receptor binding of [3H]5-HT indicated an increase in 5-HT1 receptor number in dark-reared cats with no change in affinity. This elevation was specific to the visual cortex and no changes were found in the frontal cortex as a result of dark rearing. Autoradiographic histology revealed that in the normal cat visual cortex, 5-HT1 receptors were present in all cortical layers and were slightly more dense in supragranular and infragranular layers. In dark-reared cats, there was a marked elevation in receptor density in supragranular and infragranular layers and little change within layer IV. Immunohistochemical techniques (anti-5-HT) were used to compare serotoninergic innervation in the visual cortex of normal and dark-reared cats. In normal cat visual cortex, serotonin fibers were most dense in the superficial layers (I-III), least dense in layers IV and VI, and intermediate in layer V. No differences were found between normal and dark-reared cats in the laminar distribution or density of serotoninergic innervation. These results indicate that visual experience is necessary for the normal development of the visual cortical serotonin system. The findings that the effects of dark rearing were specific to the visual cortex and that within the visual cortex these effects were specific to supra- and infragranular layers are consistent with a possible role for serotonin in the prolonged physiological plasticity that occurs in the visual cortex of dark-reared cats.

Animals↗
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

Intracellular recordings of rod responses during dark-adaptation.

1. Dark-adaptation of rod photoreceptors has been studied in the isolated axolotl (Ambystoma mexicanum) retina by intracellular recordings. Rod responsiveness was greatly reduced immediately after a 30 sec partial bleach, but partially recovered with time in the dark. 2. In parallel spectrophotometric measurements using isolated retinas, regeneration of the rod pigment could not be detected after a 30 sec bleach. 3. During rod dark-adaptation, the response of a rod to a given stimulus increased in amplitude, duration, and rate of rise but did not recover completely to the dark-adapted values. Response latency was lengthened immediately after a bleach but ultimately returned to the dark-adapted level. 4. The time courses of dark-adaptation determined on the basis of the intensity of a stimulus needed to evoke a response having a criterion amplitude, a criterion duration, or a criterion rate of rise were similar. On the other hand changes in latency of the response and magnitude of the saturated amplitude followed different time courses. Change in log threshold was found to be related to change in saturated amplitude by an exponential function during dark-adaptation. 5. After bleaching 10% or less of the rod pigment, the kinetics of both recovery of log threshold and decrease in absorbance at 400 nm (metarhodopsin II+free retinal) could be described by two concurrent first-order processes having similar time constants. However, after bleaching more than 10% of the rod pigment, changes in sensitivity and absorbance did not follow parallel time courses. 6. Metarhodopsin III cannot be solely responsible for setting the axolotl rod sensitivity since rod thresholds decrease monotonically during dark-adaptation whereas meta III concentration reaches a peak 3 min after the bleach and decreases thereafter.

Ambystoma↗
PubMed1975

Regulation of pineal rhythms in chickens: effects of blinding, constant light, constant dark, and superior cervical ganglionectomy.

Pineal serotonin N-acetyltransferase activity and melatonin content exhibit marked daily changes in chickens; peak values occur during the period of low locomotor activity which coincides with dark in a 24-hour light-dark cycle. The photic and neural regulation of these daily changes were studied by measuring pineal serotonin N-acetyl-transferase activity, hydroxyindole-O-methyltransferase (HIOMT) activity, and melatonin content in experiments in which chickens were subjected to light-dark cycles, constant light, and constant dark and were surgically blinded or superior cervical ganglionectomized. It was found that: 1) The daily changes in N-acetyltransferase activity and melatonin content appear to persist in constant dark, and they disappear in constant light. 2) The eyes are not necessary for photic control of the daily changes, and the effect of constant light on N-acetyltransferase activity and melatonin content may be non-visual, that is, the eyes not being necessary. 3) The occurrence of the daily change in N-acetyltransferase activity and melatonin content does not require the superior cervical ganglia; the persistence of the changes in constant dark, however, may require the ganglia. 4) HIOMT activity was lower in constant light than in light-dark cycles and lower still in constant dark than in constant light. Neither the presence of the eyes nor the superior cervical ganglia affected HIOMT activity, as previously reported.

Acetylserotonin O-Methyltransferase↗
PubMed1992

Effects of light and darkness on pH outside rod photoreceptors in the cat retina.

We recorded pH in the extracellular space surrounding rod photoreceptors in the dark-adapted eye of the cat and during illumination with double-barreled H(+)-selective microelectrodes. A pH of 7.17 was recorded in the vitreous at the retinal surface of the dark-adapted eye and this became more alkaline during light adaptation. In dark adaptation, a pH close to 7.00 was recorded in a region of maximal acidity in the extracellular space surrounding rods in the outer nuclear layer (ONL). pH steeply alkalinized as the microelectrode was moved more distally towards the retinal pigment epithelium (RPE), and almost reached the pH of the arterial blood at the apical surface of the RPE. Illumination produced an intraretinal alkalinization that was largest (up to 0.2 pH units) in the ONL, maximal in amplitude at rod-saturating intensities, and that was sustained during steady background illumination. The light-evoked alkalinization was relatively slow in onset, having a time constant (1/e) of 64 sec, and took 8-12.5 min to return to the dark-adapted level after the offset of maintained illumination. These results show that acid production by cat rods is highest in the dark, reflecting a high rate of energy metabolism, and suggest that glycolysis is required to support the dark current. Illumination, by suppressing both glycolysis and respiration, alkalinizes the extracellular space surrounding rods. The substantial change in pH outside rods from dark to light could alter pH dependent properties of the interphotoreceptor matrix.

Adaptation, Ocular↗
PubMed1975

Control of the rat's circadian self-stimulation rhythm by light-dark cycles.

Rats with hypothalamic and septal electrodes were maintained in continuous test environments where bar-press responses produced brief reinforcing electrical stimulations. Long-term trends in response emission were measured under continuous exposure to light, dark and 12 hr light-dark alternations. In addition, transient behavioral adjustment to sudden 180 degrees phase shifts in the light-dark schedule was studied. The ambient light condition was found to control the period and phase of the circadian rhythm of brain self-stimulation behavior, as quantified by Fourier analysis. The circadian period was greatest under constant light (up to 24.90 hr under dim illumination), and approximated 24.00 hr under constant dark. Successful nocturnal entrainment to 12 hr light-dark alternations was obtained, with the peak of the 24 hr Fourier fundamental occurring in the middle-to-late dark segments. Three to 11 days were required for re-entrainment to 180 degrees light-dark phase shifts, during which the behavioral oscillation period increased to values comparable to periods under constant light. The rate of re-entrainment appeared to be proportional to illumination intensity during light segments.

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↗
PubMed1992

Stabilization of gaze during circular locomotion in darkness. II. Contribution of velocity storage to compensatory eye and head nystagmus in the running monkey.

1. Yaw eye in head (Eh) and head on body velocities (Hb) were measured in two monkeys that ran around the perimeter of a circular platform in darkness. The platform was stationary or could be counterrotated to reduce body velocity in space (Bs) while increasing gait velocity on the platform (Bp). The animals were also rotated while seated in a primate chair at eccentric locations to provide linear and angular accelerations similar to those experienced while running. 2. Both animals had head and eye nystagmus while running in darkness during which slow phase gaze velocity on the body (Gb) partially compensated for body velocity in space (Bs). The eyes, driven by the vestibuloocular reflex (VOR), supplied high-frequency characteristics, bringing Gb up to compensatory levels at the beginning and end of the slow phases. The head provided substantial gaze compensation during the slow phases, probably through the vestibulocollic reflex (VCR). Synchronous eye and head quick phases moved gaze in the direction of running. Head movements occurred consistently only when animals were running. This indicates that active body and limb motion may be essential for inducing the head-eye gaze synergy. 3. Gaze compensation was good when running in both directions in one animal and in one direction in the other animal. The animals had long VOR time constants in these directions. The VOR time constant was short to one side in one animal, and it had poor gaze compensation in this direction. Postlocomotory nystagmus was weaker after running in directions with a long VOR time constant than when the animals were passively rotated in darkness. We infer that velocity storage in the vestibular system had been activated to produce continuous Eh and Hb during running and to counteract postrotatory afterresponses. 4. Continuous compensatory gaze nystagmus was not produced by passive eccentric rotation with the head stabilized or free. This indicates that an aspect of active locomotion, most likely somatosensory feedback, was responsible for activating velocity storage. 5. Nystagmus was compared when an animal ran in darkness and in light. the beat frequency of eye and head nystagmus was lower, and the quick phases were larger in darkness. The duration of head and eye quick phases covaried. Eye quick phases were larger when animals ran in darkness than when they were passively rotated. The maximum velocity and duration of eye quick phases were the same in both conditions. 6. The platform was counterrotated under one monkey in darkness while it ran in the direction of its long vestibular time constant.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Physiological↗
PubMed1991

Preretinal pH changes in the rabbit under conditions of light and dark.

Preretinal pH was measured in the avascular region of 19 rabbit retinas during alternating cycles of light and dark, using a miniature, needle-type pH electrode. In 14 experiments with the rabbits breathing room air, cyclic changes in pH, decreasing in the dark and increasing in the light, were observed. The transition from light to dark caused a mean pH decrease of 0.047 +/- 0.029 U (n = 14). An inversion of the light/dark pH response was observed in five experiments. In three of these, the effect was induced by having the rabbits breathe 100% O2. In the five rabbits showing a reversed response, a mean pH increase of 0.034 +/- 0.025 pH U was observed in the dark; light-ON caused a decrease of 0.035 +/- 0.025 pH U. The direction of the preretinal pH change is thought to be the net effect of light/dark-induced changes in the metabolism of the photoreceptors and inner retinal layers (defined for the purpose of this paper as the region between the outer synaptic layer and the inner limiting membrane). In six separate experiments, retinal metabolism was assessed by measuring preretinal PO2 during alternating cycles of light and dark while the rabbits breathed room air. Oxygen tension declined from a mean of 14.5 +/- 6.2 (S.D.) mmHg in the light to 10.1 +/- 5.4 (S.D.) mmHg in darkness, and increased from a mean of 10.9 +/- 5.1 (S.D.) mmHg in darkness to 15.4 +/- 5.8 (S.D.) mmHg in the light. The time courses of the pH and the PO2 changes were similar.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
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↗