Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems

Bacteria have adaptive immunity against viruses (phages) in the form of CRISPR-Cas immune systems. Currently, 6 types of CRISPR-Cas systems are known and the molecular study of three of these has revealed important molecular differences. It is unknown if and how these molecular differences change the outcome of phage infection and the evolutionary pressure the CRISPR-Cas systems faces. To determine the importance of these molecular differences, we model a phage outbreak entering a population defending exclusively with a type I/II or a type III CRISPR-Cas system. We show that for type III CRISPR-Cas systems, rapid phage extinction is driven by the probability to acquire at least one resistance spacer. However, for type I/II CRISPR-Cas systems, rapid phage extinction is characterized by an a threshold-like behaviour: any acquisition probability below this threshold leads to phage survival whereas any acquisition probability above it, results in phage extinction. We also show that in the absence of autoimmunity, high acquisition rates evolve. However, when CRISPR-Cas systems are prone to autoimmunity, intermediate levels of acquisition are optimal during a phage outbreak. As we predict an optimal probability of spacer acquisition 2 factors of magnitude above the one that has been measured, we discuss the origin of such a discrepancy. Finally, we show that in a biologically relevant parameter range, a type III CRISPR-Cas system can outcompete a type I/II CRISPR-Cas system with a slightly higher probability of acquisition.     

Savings and extinction of conditioned eyeblink responses in fragile X syndrome

The fragile X syndrome (FRAXA) is the most widespread heritable form of mental retardation caused by the lack of expression of the fragile X mental retardation protein (FMRP). This lack has been related to deficits in cerebellum-mediated acquisition of conditioned eyelid responses in individuals with FRAXA. In the present behavioral study, long-term effects of deficiency of FMRP were investigated by examining the acquisition, savings and extinction of delay eyeblink conditioning in male individuals with FRAXA. In the acquisition experiment, subjects with FRAXA displayed a significantly poor performance compared with controls. In the savings experiment performed at least 6 months later, subjects with FRAXA and controls showed similar levels of savings of conditioned responses. Subsequently, extinction was faster in subjects with FRAXA than in controls. These findings confirm that absence of the FMRP affects cerebellar motor learning. The normal performance in the savings experiment and aberrant performance in the acquisition and extinction experiments of individuals with FRAXA suggest that different mechanisms underlie acquisition, savings and extinction of cerebellar motor learning.     

Species immigration, extinction and turnover of vascular plants in boreal lakes

Dictated by limited resource availability for land acquisition, a central question in conservation biology is the ability of areas of different size to maintain species diversity. The selected reserves should not only be species rich at the moment, but should also maintain species diversity in the long run. We used two sets of data on vascular plant species in boreal lakes collected in 1933/34 and 1996 to test the relationships between lake area and the extinction, immigration and turnover rates of the species. Moreover, we investigated, whether the number of species in 1933/34 or water connection between lakes was related to extinction, immigration and turnover rates of species. We found that lake area or shoreline length was not correlated with immigration or turnover rate. But extinction rate was slightly negatively correlated with shoreline length. The original number of species was positively related to the number of species extinctions and to the absolute turnover rate in the lakes, which indicates that species richness does not create stability in these communities. Species number was not correlated with immigration rate. Upstream water connections in the lakes did not affect immigration, extinction or turnover rates. We conclude that length of the shoreline is a better measure of suitable area for water plants than the lake area, and that because the correlation between shoreline length and extinction rate was slight, also small lakes can be valuable for conservation.     

Is extinction the hallmark of operant discrimination?: Reinforcement and S effects

Using a successive discrimination procedure with rats, three experiments investigated the contribution of reinforcement rate and amount of S(Delta) exposure on the acquisition of an operant discrimination. S(D) components and were always 2 min in length, while S(Delta) (extinction) components were either 1 min or 4 min in length; responses in S(D) were reinforced on one of four schedules. In Experiment 1, each of eight groups were exposed to one possible combination of rate of reinforcement and S(Delta) component length. At every level of reinforcement, the 4 min S(Delta) groups acquired the discrimination more quickly. However, within each level of reinforcement, the proportions of responding in S(D) as a function cumulative S(Delta) exposure were equivalent, regardless of the number of reinforcers earned in S(D), suggesting that extinction is the "hallmark" of discrimination. Experiment 2 sought to replicate these results in a within-subjects design, and although the 4 min S(Delta) conditions always produced superior discriminations, the lack of discriminated responding in some conditions suggested that stimulus disparity was reduced. Experiment 3 clarified those results and extended the finding that the acquisition of operant discrimination closely parallels extinction of responding in S(Delta). In sum, it appears that higher reinforcement rates and longer S(Delta) exposure facilitate the acquisition of discriminated operant responding.     

Exposure to estradiol before but not during acquisition of LiCl-induced conditioned taste avoidance accelerates extinction

Estradiol accelerates extinction of LiCl-induced conditioned taste avoidance when it is present continuously before and during acquisition. We have suggested that the effect of estradiol on extinction is due to its illness-associated, rather than learning-associated, properties. If this were the case, then one would expect estradiol to act before but not during acquisition. This expectation is based on previous work showing attenuation of learned taste avoidance when rats are given distal preexposure (greater than 24 h before conditioning) or proximal preexposure (less than 24 h before conditioning) to the illness-inducing agent LiCl before acquisition of a LiCl-induced conditioned taste avoidance. In three separate experiments, estradiol was administered during three different time periods via subcutaneous implantation of a 10-mm estradiol-filled capsule. In each experiment, the extinction of estradiol-treated females was compared to that of females implanted with empty capsules. In the first experiment, female rats were given distal exposure to estradiol before acquisition. Capsules were implanted 11 days before acquisition and were removed 2 days before acquisition. In the second experiment, female rats were given proximal exposure to estradiol before acquisition. Capsules were implanted 2.5 h before LiCl was paired with a sucrose solution and were removed 16.5 h later. In the third experiment, female rats were given exposure to estradiol during acquisition. Capsules were implanted at the same time as LiCl administration and were removed 18 h later. The only estradiol-treated females to show accelerated extinction were those given distal preexposure to estradiol in Experiment 1. These data do not support a learning-associated hypothesis and only partially support an illness-associated hypothesis. The failure to find accelerated extinction following proximal preexposure may reflect an inappropriate choice of the parameters used in the experiment or a difference in the stimulus properties of LiCl and estradiol that allow each to serve as conditioning and preexposure agents in conditioned taste avoidance paradigms [corrected].     

Extinction learning in humans: role of the amygdala and vmPFC

Understanding how fears are acquired is an important step in translating basic research to the treatment of fear-related disorders. However, understanding how learned fears are diminished may be even more valuable. We explored the neural mechanisms of fear extinction in humans. Studies of extinction in nonhuman animals have focused on two interconnected brain regions: the amygdala and the ventral medial prefrontal cortex (vmPFC). Consistent with animal models suggesting that the amygdala is important for both the acquisition and extinction of conditioned fear, amygdala activation was correlated across subjects with the conditioned response in both acquisition and early extinction. Activation in the vmPFC (subgenual anterior cingulate) was primarily linked to the expression of fear learning during a delayed test of extinction, as might have been expected from studies demonstrating this region is critical for the retention of extinction. These results provide evidence that the mechanisms of extinction learning may be preserved across species.     

Effects of cholecystokinin octapeptide sulphate ester and unsulphated cholecystokinin octapeptide on active avoidance behaviour in rats

The effects of peripherally administered cholecystokinin octapeptide sulphate ester and its unsulphated form on the active avoidance behaviour of rats were studied. The acquisition of avoidance behaviour was impaired, while extinction was facilitated, following cholecystokinin octapeptide sulphate ester or unsulphated cholecystokinin octapeptide treatment. These peptides had no action on open-field activity. It is concluded that peripherally administered cholecystokinin octapeptide influences acquisition and extinction of active avoidance behaviour and this effect is unrelated to general motor activity of the animals.     

Functional gene polymorphisms in the serotonin system and traumatic life events modulate the neural basis of fear acquisition and extinction

Fear acquisition and extinction are crucial mechanisms in the etiology and maintenance of anxiety disorders. Moreover, they might play a pivotal role in conveying the influence of genetic and environmental factors on the development of a (more or less) stronger proneness for, or resilience against psychopathology. There are only few insights in the neurobiology of genetically and environmentally based individual differences in fear learning and extinction. In this functional magnetic resonance imaging study, 74 healthy subjects were investigated. These were invited according to 5-HTTLPR/rs25531 (S+ vs. L(A)L(A); triallelic classification) and TPH2 (G(-703)T) (T+ vs. T-) genotype. The aim was to investigate the influence of genetic factors and traumatic life events on skin conductance responses (SCRs) and neural responses (amygdala, insula, dorsal anterior cingulate cortex (dACC) and ventromedial prefrontal cortex (vmPFC)) during acquisition and extinction learning in a differential fear conditioning paradigm. Fear acquisition was characterized by stronger late conditioned and unconditioned responses in the right insula in 5-HTTLPR S-allele carriers. During extinction traumatic life events were associated with reduced amygdala activation in S-allele carriers vs. non-carriers. Beyond that, T-allele carriers of the TPH2 (G(-703)T) polymorphism with a higher number of traumatic life events showed enhanced responsiveness in the amygdala during acquisition and in the vmPFC during extinction learning compared with non-carriers. Finally, a combined effect of the two polymorphisms with higher responses in S- and T-allele carriers was found in the dACC during extinction. The results indicate an increased expression of conditioned, but also unconditioned fear responses in the insula in 5-HTTLPR S-allele carriers. A combined effect of the two polymorphisms on dACC activation during extinction might be associated with prolonged fear expression. Gene-by-environment interactions in amygdala and vmPFC activation may reflect a neural endophenotype translating genetic and adverse environmental influences into vulnerability for or resilience against developing affective psychopathology.     

The active avoidance reaction of laboratory rats: differences between experiments carried out in the phase of motor activity and inactivity

The influence of two phases of the circadian cycle (motor activity and motor inactivity) on the rate of acquisition and extinction of an active avoidance reaction was studied in 35-day-old male laboratory rats reared in cages (with limited social contacts), in young reared from the age of 15 days in communities (with the broad social contacts typical of this species) and in adult males reared in cages. A difference was found between the results of experiments carried out in the morning (during the motor inactivity period) and in the early evening (at the outset of the motor activity period) in both young and adult animals. The factor deciding whether acquisition or extinction was influenced depended on the mode of life. In animals reared in cages, inhibition was influenced; extinction was elaborated faster in the evening in adult animals and juvenile young were capable of 100% extinction only in the evening (in the morning only 50%). Community young achieved 100% extinction in both cases. In young rats which lived in a community from the 15th day, acquisition was influenced (it was achieved faster in the evening). The correlation between the rate of acquisition and extinction in cage-bred adult and young rats was negative if the experiments were carried out in the morning and was positive in evening experiments on young animals. In community-bred young it was positive in both cases.     

Effects of propranolol on acquisition and retrieval of morphine- induced conditioned place preference memories in ICR mice

To interfere with the drug-cue memory processes of addicts such as reconsolidation by the administration of the β-adrenergic receptor (β-AR) of norepinephrine (NE) antagonist propranolol (PRO) has become a potential therapy in the future to decrease or inhibit relapse. However, the relationship between PRO and the acquisition or retrieval of morphine-cue memory is not clear. This study examined the effects of PRO on the acquisition and retrieval of memories in morphine-induced conditioned place preference (CPP) mice model. We found that during memory acquisition period, PRO had no effects on the expression and extinction of morphine-CPP, which suggests that the β-AR was irrelevant to the CPP memory acquisition. However, during memory retrieval period, although PRO did not affect the expression of CPP, but it delayed the occurrence of CPP extinction, which indicates that PRO has an inhibit effect on CPP memory extinction, and β-AR plays an important role in modulating the extinction of morphine-CPP. Our study further improved the relationship between drug addiction and β-AR, and proposed a new theory to help developing potential therapy to cure addiction and other neuropsychiatric disorders.     

Effects of naloxone on pavlovian conditioning of eyeblink and heart rate responses in rabbits

Albino rabbits were subjected to aversive Pavlovian conditioning and extinction of eyeblink and heart rate responses. Naloxone administration had no effect on acquisition of the eyeblink response but increased responding during extinction. Naloxone also attenuated the bradycardiac heart rate CR, suggesting that endogenous opioids may be involved in mediating this response.     

Isolated effects of number of acquisition trials on extinction of rat conditioned approach behavior

Four conditioned approach experiments with rats assessed for effects of number of acquisition trials on extinction of conditioned responding, when number of acquisition sessions and total acquisition time were held constant. In Experiment 1, 32 trials per acquisition session led to more extinction responding than did 1 or 2 trials per session but less than did 4 trials per session. In Experiment 2, 2 trials per acquisition session led to more spontaneous recovery than did 32 trials per session. These latter findings are reminiscent of the overtraining extinction effect (OEE). Experiment 3 attempted to reduce the OEE with a preconditioning phase of partial reinforcement. Experiment 4 attempted to reduce the beneficial within-subject effects of increasing the number of acquisition trials on extinction observed by Gottlieb and Rescorla (2010) by extinguishing stimuli in different sessions. Overall, results suggest a procedural asymmetry: between-subject, increasing the number of trials between any pair of trials does not lead to greater persistence of responding during extinction; within-subject, it does. Results are discussed from an associative perspective, with a focus on explanations involving either frustration or comparator mechanisms, and from an information processing perspective, with a focus on Rate Estimation Theory.     

Estradiol accelerates extinction of lithium chloride-induced conditioned taste aversions through its illness-associated properties

Estradiol accelerates extinction of LiCl-induced conditioned taste aversions when it is present during a period that starts 2-3 days after acquisition and extends throughout extinction (before and during extinction). It has been suggested that estradiol acts before, not during, extinction and that its effect on extinction is associated with its illness-inducing properties. This hypothesis is based on previous work which shows an attenuation of conditioned taste aversion learning when rats are exposed to illness-inducing agents during a period that starts 2 days after acquisition and ends 2 days before extinction trials are initiated. Four experiments were designed to test elements of this hypothesis. The first two experiments demonstrated that if an estradiol-filled Silastic capsule is implanted before extinction of a LiCl-induced aversion, when the conditioned taste is not present, it accelerates extinction, but if it is implanted during extinction, when the conditioned taste is present, it prolongs extinction. The third experiment showed that the same dose of estradiol that accelerates extinction of a LiCl-induced aversion was effective in producing a conditioned taste aversion when it was present for 18 h after consumption of a novel sucrose solution. The fourth experiment indicated that serum levels of estradiol were elevated during the 18 h. These results are consistent with the hypothesis that the acceleration of extinction by estradiol is associated with its illness-inducing properties. It is suggested that estradiol acts on neural areas that mediate illness information and that one of these areas, the area postrema is necessary for estradiol to accelerate extinction of a LiCl-induced aversion.     

Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ～600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ～34 Ma, but also elevated extinction ～10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.     

Inhibiting DNA methylation alters olfactory extinction but not acquisition learning in Apis cerana and Apis mellifera

DNA methylation plays a key role in invertebrate acquisition and extinction memory. Honey bees have excellent olfactory learning, but the role of DNA methylation in memory formation has, to date, only been studied in Apis mellifera. We inhibited DNA methylation by inhibiting DNA methyltransferase (DNMT) with zebularine (zeb) and studied the resulting effects upon olfactory acquisition and extinction memory in two honey bee species, Apis cerana and A. mellifera. We used the proboscis extension reflex (PER) assay to measure memory. We provide the first demonstration that DNA methylation is also important in the olfactory extinction learning of A. cerana. DNMT did not reduce acquisition learning in either species. However, zeb bidirectionally and differentially altered extinction learning in both species. In particular, zeb provided 1 h before acquisition learning improved extinction memory retention in A. mellifera, but reduced extinction memory retention in A. cerana. The reasons for these differences are unclear, but provide a basis for future studies to explore species-specific differences in the effects of methylation on memory formation.     

Differential effects of DGAVP on acquisition and extinction of active avoidance behavior

DGAVP facilitates consolidation and retrieval of active and passive avoidance behavior. In this study it was tested whether the long-term behavioral effects of DGAVP are the consequence of an initial increase in behavioral arousal during the learning phase. Animals that were preestimated in an open field test to be low active showed a lower number of conditioned avoidance responses (CAR's) during acquisition and extinction of a shuttle-box task than high active rats. DGAVP was administered 40 min prior to the 1st acquisition session. The immediate effect of DGAVP was a shift in the bell-shaped curve of the relation between arousal and performance (13); an increase in acquisition performance was observed with a low dose of DGAVP (0.1 microgram), while a decrease was found with a high dose of DGAVP (1 microgram). A dose-dependent inhibition of extinction was found in both low and high active animals. These results suggest an immediate effect of DGAVP on the rate of acquisition behavior, which may be a direct consequence of its arousing properties, and a long-term effect on extinction, indicating the formation of memory traces specific for vasopressin-related neuropeptides.     

Extinction and colonization processes in subpopulations of five neotropical small mammal species

We report the extinction and colonization rates of five sympatric small mammal species at a semiarid locality in north central Chile. We provide information based on 6 years of monitoring on how colonization and extinction rates change according to landscape features (slope aspect) and on their relationship to populations size, population variability, and body size. We found that: (1) for all species in the assemblage, extinction rates of subpopulations from equatorial-facing slopes were significantly lower than those in polar-facing slopes, (2) population size was the most important factor determining extinction rates, (3) colonization rates did not vary between slopes, and were affected by population size only in equatorial-facing slopes, and (4) most species had higher extinction than colonization rates. Persistence of the metapopulation system for all five small mammal species appears to be fueled by repeated colonization events.     

Effects of inter-trial interval length on food-hoarding partial reinforcement of running behaviour in the golden hamster

Food-hoarding provides an adequate motivation in sated hamsters for the acquisition of a two-way running response. This learning was studied using a discrete-trial procedure, in continuous (CR) and partial reinforcement (PR) conditions, with two different inter-trial interval (ITI) lengths. The dependent variables were: the time spent by Ss in the goal section of the runway, and the number of their runs during extinction.The PR training had two effects on goal times: a slow decrease in acquisition on non-reinforced trials, and then a stabilization at this level during the extinction phase, as contrasted with the sudden increase found in CR-trained Ss when they were switched from acquisition to extinction conditions. However, the PR effects on number of runs depended upon ITI length: resistance to extinction of PR-trained Ss was superior to that of CR-trained Ss with spaced, but not with massed, trials. In the latter case, CR-trained Ss persisted as much as did PR-trained Ss. An hypothesis is offered, along the lines of the Frustration theory.     

Historical bird and terrestrial mammal extinction rates and causes

Aim Conservation of species is an ongoing concern. Location Worldwide. Methods We examined historical extinction rates for birds and mammals and contrasted island and continental extinctions. Australia was included as an island because of its isolation. Results Only six continental birds and three continental mammals were recorded in standard databases as going extinct since 1500 compared to 123 bird species and 58 mammal species on islands. Of the extinctions, 95% were on islands. On a per unit area basis, the extinction rate on islands was 177 times higher for mammals and 187 times higher for birds than on continents. The continental mammal extinction rate was between 0.89 and 7.4 times the background rate, whereas the island mammal extinction rate was between 82 and 702 times background. The continental bird extinction rate was between 0.69 and 5.9 times the background rate, whereas for islands it was between 98 and 844 times the background rate. Undocumented prehistoric extinctions, particularly on islands, amplify these trends. Island extinction rates are much higher than continental rates largely because of introductions of alien predators (including man) and diseases. Main conclusions Our analysis suggests that conservation strategies for birds and mammals on continents should not be based on island extinction rates and that on islands the key factor to enhance conservation is to alleviate pressures from uncontrolled hunting and predation.     

Resting Heart Rate Variability Predicts Safety Learning and Fear Extinction in an Interoceptive Fear Conditioning Paradigm

This study aimed to investigate whether interindividual differences in autonomic inhibitory control predict safety learning and fear extinction in an interoceptive fear conditioning paradigm. Data from a previously reported study (N = 40) were extended (N = 17) and re-analyzed to test whether healthy participants'' resting heart rate variability (HRV) - a proxy of cardiac vagal tone - predicts learning performance. The conditioned stimulus (CS) was a slight sensation of breathlessness induced by a flow resistor, the unconditioned stimulus (US) was an aversive short-lasting suffocation experience induced by a complete occlusion of the breathing circuitry. During acquisition, the paired group received 6 paired CS-US presentations; the control group received 6 explicitly unpaired CS-US presentations. In the extinction phase, both groups were exposed to 6 CS-only presentations. Measures included startle blink EMG, skin conductance responses (SCR) and US-expectancy ratings. Resting HRV significantly predicted the startle blink EMG learning curves both during acquisition and extinction. In the unpaired group, higher levels of HRV at rest predicted safety learning to the CS during acquisition. In the paired group, higher levels of HRV were associated with better extinction. Our findings suggest that the strength or integrity of prefrontal inhibitory mechanisms involved in safety- and extinction learning can be indexed by HRV at rest.