Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis.

Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.

Cell type-specific translational profiling in the Xenopus laevis retina.

BACKGROUND: Translating Ribosome Affinity Purification (TRAP), a method recently developed to generate cell type-specific translational profiles, relies on creating transgenic lines of animals in which a tagged ribosomal protein is placed under regulatory control of a cell type-specific promoter. An antibody is then used to affinity purify the tagged ribosomes so that cell type-specific mRNAs can be isolated from whole tissue lysates. RESULTS: Here, cell type-specific transgenic lines were generated to enable TRAP studies for retinal ganglion cells and rod photoreceptors in the Xenopus laevis retina. Using real time quantitative PCR for assessing expression levels of cell type-specific mRNAs, the TRAP method was shown to selectively isolate mRNAs expressed in the targeted cell and was efficient at purifying mRNAs expressed at both high and low levels. Statistical measures used to distinguish cell type-specific RNAs from low level background and non-specific RNAs showed TRAP to be highly effective in Xenopus. CONCLUSIONS: TRAP can be used to purify mRNAs expressed in rod photoreceptors and retinal ganglion cells in X. laevis. The generated transgenic lines will enable numerous studies into the development, disease, and injury of the X. laevis retina.

Neurotrophins use the Erk5 pathway to mediate a retrograde survival response.

Growth factors synthesized and released by target tissues promote survival and differentiation of innervating neurons. This retrograde signal begins when growth factors bind receptors at nerve terminals. Activated receptors are then endocytosed and transported through the axon to the cell body. Here we show that the mitogen-activated protein kinase (MAPK) signaling pathways used by neurotrophins during retrograde signaling differ from those used following direct stimulation of the cell soma. During retrograde signaling, endocytosed neurotrophin receptors (Trks) activate the extracellular signal-related protein kinase 5 (Erk5) pathway, leading to nuclear translocation of Erk5, phosphorylation of CREB, and enhanced neuronal survival. In contrast, Erk1/2, which mediates nuclear responses following direct cell body stimulation, does not transmit a retrograde signal. Thus, the Erk5 pathway has a unique function in retrograde signaling. Differential activation of distinct MAPK pathways may enable an individual growth factor to relay information that specifies the location and the nature of stimulation.

HSP70 expression is increased during the day in a diurnal animal, the golden-mantled ground squirrel Spermophilus lateralis.

Heat shock protein 70 (HSP70) gene expression was studied in a seasonal hibernator, the diurnal ground squirrel, Spermophilus lateralis. RNA transcripts of 2.7 and 2.9 kb hybridizing to an HSP70 cDNA were expressed in both brain and peripheral tissues of pre-hibernation euthermic animals; higher levels of expression were observed during the day than during nighttime samples. A decline in the expression of both transcripts occurred in all tissues examined during hibernation that remained low throughout the hibernation season, including the interbout euthermic periods and regardless of time of day. Quantitative comparisons showed pre-hibernation nighttime HSP70 expression to be as low as that observed during hibernation, despite the drastic increase in metabolic state and nearly 30 degrees C difference in body temperature. In contrast to HSP70, some mRNAs, such as beta-actin and HSP60, remained relatively constant, while others, such as glyceraldehyde 3-phosphate dehydrogenase, increased in specific tissues during the hibernation season. These results indicate that the expression of a highly conserved gene involved in protection from cellular stress, HSP70, can vary with an animal's arousal state.

Rapid nuclear responses to target-derived neurotrophins require retrograde transport of ligand-receptor complex.

Target-derived neurotrophins initiate signals that begin at nerve terminals and cross long distances to reach the cell bodies and regulate gene expression. Neurotrophin receptors, Trks, themselves serve as retrograde signal carriers. However, it is not yet known whether the retrograde propagation of Trk activation reflects movement of Trk receptors from neurites to cell bodies or reflects serial activation of stationary Trk molecules. Here, we show that neurotrophins selectively applied to distal neurites of sensory neurons rapidly induce phosphorylation of the transcription factor cAMP response element-binding protein (CREB) and also cause a slower increase in Fos protein expression. Both nuclear responses require activation of neurotrophin receptors (Trks) at distal nerve endings and retrograde propagation of Trk activation to the nerve cell bodies. Using photobleach and recovery techniques to follow biologically active, green fluorescent protein (GFP)-tagged BDNF receptors (TrkB-GFP) in live cells during retrograde signaling, we show that TrkB-GFP moves rapidly from neurites to the cell bodies. This rapid movement requires ligand binding, Trk kinase activity, and intact axonal microtubules. When they reach the cell bodies, the activated TrkB receptors are in a complex with ligand. Thus, the retrograde propagation of activated TrkB from neurites to cell bodies, although rapid, reflects microtubule-dependent transport of phosphorylated Trk-ligand complexes. Moreover, the relocation of activated Trk receptors from nerve endings to cell bodies is required for nuclear signaling responses. Together, these data support a model of retrograde signaling whereby rapid vesicular transport of ligand-receptor complex from the neurites to the cell bodies mediates the nuclear responses.

Gene expression in the brain across the hibernation cycle.

The purpose of this study was to characterize changes in gene expression in the brain of a seasonal hibernator, the golden-mantled ground squirrel, Spermophilus lateralis, during the hibernation season. Very little information is available on molecular changes that correlate with hibernation state, and what has been done focused mainly on seasonal changes in peripheral tissues. We produced over 4000 reverse transcription-PCR products from euthermic and hibernating brain and compared them using differential display. Twenty-nine of the most promising were examined by Northern analysis. Although some small differences were observed across hibernation states, none of the 29 had significant changes. However, a more direct approach, investigating expression of putative hibernation-responsive genes by Northern analysis, revealed an increase in expression of transcription factors c-fos, junB, and c-Jun, but not junD, commencing during late torpor and peaking during the arousal phase of individual hibernation bouts. In contrast, prostaglandin D2 synthase declined during late torpor and arousal but returned to a high level on return to euthermia. Other genes that have putative roles in mammalian sleep or specific brain functions, including somatostatin, enkephalin, growth-associated protein 43, glutamate acid decarboxylases 65/67, histidine decarboxylase, and a sleep-related transcript SD464 did not change significantly during individual hibernation bouts. We also observed no decline in total RNA or total mRNA during torpor; such a decline had been previously hypothesized. Therefore, it appears that the dramatic changes in body temperature and other physiological variables that accompany hibernation involve only modest reprogramming of gene expression or steady-state mRNA levels.

TrkA glycosylation regulates receptor localization and activity.

The human nerve growth factor receptor (TrkA) contains four potential N-glycosylation sites that are highly conserved within the Trk family of neurotrophin receptors, and nine additional sites that are less well conserved. Using a microscale deglycosylation assay, we show here that both conserved and variable N-glycosylation sites are used during maturation of TrkA. Glycosylation at these sites serves two distinct functions. First, glycosylation is necessary to prevent ligand-independent activation of TrkA. Unglycosylated TrkA core protein is phosphorylated even in the absence of ligand stimulation and displays constitutive kinase activity as well as constitutive interaction with the signaling molecules Shc and PLC-gamma. Second, glycosylation is required to localize TrkA to the cell surface, where it can trigger the Ras/Raf/MAP kinase cascade. Using confocal microscopy, we show that unglycosylated active Trk receptors are trapped intracellularly. Furthermore, the unglycosylated active TrkA receptors are unable to activate kinases in the Ras-MAP kinase pathway, MEK and Erk. Consistent with these biochemical observations, unglycosylated TrkA core protein does not promote neuronal differentiation in Trk PC12 cells even at high levels of constitutive catalytic activity.

The effects of practice on object-based, location-based, and static-display inhibition of return.

We report two experiments that examine the effects of practice on object-based, location-based, and static-display inhibition of return (IOR). The results are clear: All three effects get smaller with practice. These findings are at odds with the results of Müller and von Mühlenen (1996), who failed to observe object-based IOR and detected no effect of practice on static-display IOR. However, their subjects were more practiced than ours prior to data collection. We suggest, therefore, that the reducing effect of practice on IOR have occurred in their unrecorded practice sessions. We also discuss a two-process model in which IOR is seen as the net effect of underlying inhibitory and excitatory processes. In such models (e.g., Solomon & Corbit, 1974), practice often results in a reduction of the net effect of the two processes.

Trk receptors function as rapid retrograde signal carriers in the adult nervous system.

During development target-derived neurotrophins promote the survival of neurons. However, mature neurons no longer depend on the target for survival. Do target-derived neurotrophins retain retrograde signaling functions in mature neurons, and, if so, how are they executed? We addressed this question by using a phosphotyrosine-directed antibody to locate activated Trk receptors in adult rat sciatic nerve. We show that catalytically active Trk receptors are located within the axon of adult rat sciatic nerve and that they are distributed throughout the length of the axons. These catalytically active receptors are phosphorylated on tyrosine at a position that couples them to the signal-generating proteins Ras and PI3 kinase. Neurotrophin applied at sciatic nerve terminals increases both catalytic activity and phosphorylation state of Trk receptors at distant points within the axons. Trk activation initiated at the nerve terminals propagates through the axon toward the nerve cell body at an initial rate that exceeds that of conventional vesicular transport. However, our data suggest that this rapid signal is nevertheless vesicle-associated. Thus, in mature nerves, activated Trk receptors function as rapid retrograde signal carriers to execute remote responses to target-derived neurotrophins.

Daily variation of CNS gene expression in nocturnal vs. diurnal rodents and in the developing rat brain.

Expression of c-fos has been shown to vary throughout the brain over the course of the 24-h day. The magnitude of these changes appear to be similar in a light:dark (LD) cycle or in constant dark (DD). To further examine whether the diurnal and circadian changes in c-fos and other immediate-early gene (IEG) expression in brain are related to waking behaviors such as locomotor activity, we conducted three experiments using Northern analysis. First, we compared IEG expression in nocturnal vs. diurnally active species. Second, we investigated IEG expression in a hibernating species during its active and inactive phases. Third, we examined the development of IEG expression in the young post-natal rat. As a comparison to results obtained in extra-SCN brain regions, we also examined IEG and vasopressin expression in the SCN itself across the circadian cycle. Animals maintained under a 12:12-h LD cycle were sacrificed in the morning (10:00-11:00 h, ZT2-ZT3) or night (22:00-23:00 h, ZT14-ZT15) or at the corresponding circadian times (CT) when kept in DD. Rats sacrificed in the morning always showed lower c-fos expression than at night in all brain areas examined while the reverse pattern was seen in squirrels under both LD and DD conditions, suggesting a direct correlation between c-fos message and activity. The cerebellum displayed the greatest magnitude change between morning and night (often reaching 10-fold). Among other IEGs examined, the expression of NGFI-A and junB are similar to c-fos, but of lesser magnitude, whereas c-jun appears to be invariant in the rat but is increased during the active phase in squirrels. During the hibernation season, squirrels have lower levels of c-fos consistent with their low levels of activity even during their euthermic interbout periods. c-fos expression in the cerebellum and rest of brain of 1-week-old rats sacrificed at ZT3 and ZT15 showed low levels at both timepoints whereas 2- and 3-week-old animals had higher levels at night as do adults. Among other IEGs, junB and NGFI-A again were similar to c-fos while c-jun and junD were more constant. Our observations support the idea of a diurnal rhythm of IEG expression in the CNS that is related to waking behaviors. Among IEGs, c-fos exhibits the greatest daily variation in expression.

Brief Report Reduced Negative Priming in Schizotypal Subjects does reflect Reduced Cognitive Inhibition.

Numerous studies have suggested, via the interpretation of the negative priming effect as a measure of cognitive inhibition, that schizotypal subjects are less able to inhibit irrelevant distracting information. Recent research has revealed, however, that negative priming effects can be caused by two quite different processes: distractor inhibition and perceptual review. Therefore, unequivocal conclusions concerning less efficient inhibition in schizotypal individuals are not possible from previous research. The present experiment minimises the contribution of perceptual review to negative priming and demonstrates that when a purer measure of inhibition is taken, schizotypal subjects are indeed less able to inhibit irrelevant distracting stimuli.

Inhibition of return to successively cued spatial locations: commentary on Pratt and Abrams (1995).

J. Pratt and R.A. Abrams (1995) reported that the inhibition of return of attention is found only for the most recently attended of 2 cued locations. This study does not dispute their findings, but suggests that a more ecologically valid experiment would have more than 2 possible target locations. Twelve male students participated in an experiment in which the target may occur in 1 of 4 possible locations, after 3 of those locations have been cued exogenously in sequence. Inhibition of return was found for each of the cued locations. This result suggests that inhibition may be an important mechanism for aiding visual search in complex environments.

The effects of sub-anaesthetic doses of ketamine on memory, cognitive performance and subjective experience in healthy volunteers.

The cognitive and subjective effects of sub-anaesthetic doses of ketamine on healthy volunteers were examined. Twelve healthy volunteers received 25 mg ketamine, 10 mg ketamine and saline placebo, i.m. in a double-blind, Latin square design. A cognitive, perceptual and self-report test battery was administered over 45 min. The order of tests was rotated to control for timing effects. Ketamine (25 mg) significantly affected verbal learning and memory, parallel visual search, some measures of psychomotor performance, measures of arousal, subjective mood ratings and visual perception. Measures of attention and frontal lobe functioning were relatively unaffected. Thus, low doses of ketamine had selective, dose-related effects on memory, perceptual and psychomotor functions. The disruption of memory and perceptual processes may help to explain the unique subjective state induced by ketamine.

C-fos mRNA increases in the ground squirrel suprachiasmatic nucleus during arousal from hibernation.

During hibernation the body temperature of the golden-mantled ground squirrel, Spermophilus lateralis, may drop below 5 degrees C for a few hours to a week or more. Animals cycle between euthermia and deep hibernation many times over the course of the hibernation season. Expression of the transcription factor c-fos increased in the suprachiasmatic nucleus (SCN) of the hypothalamus, the mammalian circadian clock, during deep hibernation and peaked during the arousal from hibernation. The pattern of increase in c-fos messenger RNA seen in the SCN by in situ hybridization was similar to that seen by Northern blot analysis of total hypothalamic RNA. The induction of c-fos may reflect a wake-up signal, increasing transcription of genes required in the euthermic state.

Immediate early gene expression in brain during sleep deprivation: preliminary observations.

The two-process model of sleep regulation posits that a homeostatic drive to sleep, referred to as Process S, increases with time spent awake. The purpose of this study was to evaluate whether immediate early gene (IEG) expression increases in the brain in proportion to time spent awake, when Process S would be expected to increase. Rats were deprived of sleep by cage tapping, cage rotation and gentle handling beginning at light onset for 45 minutes, 3 hours or 6 hours. At the end of the deprivation periods, deprived animals and an equal number of controls were decapitated, the brains dissected into subregions and frozen. Northern blots were prepared from cortex, thalamus, cerebellum, pons and hypothalamus and hybridized with cDNA probes to five IEG mRNAs; c-fos, c-jun, junB, NGFI-A and NGFI-B. Basal levels of c-fos mRNA were detectable in all brain regions from all animals. Sleep-deprived animals showed higher expression of c-fos mRNA than control animals following 45 minutes and 6 hours of sleep deprivation in all brain regions examined, with the greatest increases observed in the cerebellum. Surprisingly, only the pons and cerebellum showed clear increases at the 3-hour timepoint. In contrast to c-fos, c-jun mRNA was essentially invariant among the animals while junB mRNA was inconsistently elevated. The expression of NGFI-A and NGFI-B was similar to the c-fos pattern but of lesser magnitude.(ABSTRACT TRUNCATED AT 250 WORDS)

Independence of the circadian rhythm in alertness from the sleep/wake cycle.

It is common knowledge that our feelings of alertness or drowsiness vary throughout the day. Indeed, this diurnal variation is so widely accepted that it has been used to validate the drowsy/alert component of activation obtained from mood adjective checklists. There is, however, some evidence from sleep deprivation and shiftwork studies that this variation is not simply a reflection of our sleep/wake cycle, as might be expected, but is at least partially dependent on an endogenous circadian (approximately 24 h) oscillator such as that proposed to account for the circadian rhythm in body temperature and other physiological variables. Here we have tested this suggestion by separating the body-temperature rhythm from the sleep/wake cycle by progressively shortening artificial time cues (zeitgebers). Our results indicate that the circadian rhythm in alertness can become independent of both the sleep/wake cycle and the rhythm in body temperature. Further, and contrary to our expectations, the results suggest that the sleep/wake cycle exerts less influence on the alertness rhythm than it does on that of temperature.