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PubMed1996

Sudden and Gradual Molluscan Extinctions in the Latest Cretaceous of Western European Tethys

Incompleteness of the fossil record has confounded attempts to establish the role of the end-Cretaceous bolide impact in the Late Cretaceous mass extinctions. Statistical analysis of latest Cretaceous outer-shelf macrofossils from western European Tethys reveals (i) a major extinction at or near the Cretaceous-Tertiary (K-T) boundary, probably caused by the impact, (ii) either a faunal abundance change or an extinction of up to nine ammonite species associated with a regression event shortly before the boundary, (iii) gradual extinction of most inoceramid bivalves well before the K-T boundary, and (iv) background extinction of approximately six ammonites throughout the latest Cretaceous.

Journal Article↗
PubMed1993

Extinction of Oct-3/4 gene expression in embryonal carcinoma x fibroblast somatic cell hybrids is accompanied by changes in the methylation status, chromatin structure, and transcriptional activity of the Oct-3/4 upstream region.

In this study we evaluate, for the first time, the molecular mechanism that underlies the extinction of a tissue-specific transcription factor, Oct-3/4, in somatic cell hybrids and compared it with its down-regulation in retinoic acid (RA)-treated embryonal carcinoma (EC) cells. The Oct-3/4 gene, which belongs to the POU family of transcription factors and is abundantly expressed in EC (OTF9-63) cells, provides an excellent model system with which to study the extinction phenomenon. Unlike other genes whose expression has been repressed in hybrid cells but not during in vivo differentiation, Oct-3/4 expression is dramatically repressed in OTF9-63 x fibroblast hybrids and also during embryogenesis. The ectopic expression of Oct-3/4 in hybrid cells under a constitutive promoter is sufficient for transcriptional activation of an octamer-dependent promoter. These results argue against the possibility that fibroblasts contain a direct repressor which binds directly to the octamer sequence and prevents Oct-3/4 protein from binding. The extinction of Oct-3/4 binding activity in the hybrid cells occurs at the level of mRNA transcription, similarly to the repression of Oct-3/4 transcription during in vivo differentiation. This shutdown of Oct-3/4 transcription in hybrid cells and in RA-treated EC cells is accompanied by de novo methylation of its 1.3-kb upstream region. In contrast to EC cells, in which this region is sensitive to MspI digestion, in hybrid cells and in RA-treated EC cells, the Oct-3/4 upstream region is resistant to MspI digestion, which suggests a change in its chromatin structure. Furthermore, extinction is not restricted to the endogenous Oct-3/4 gene but is also exerted upon a transiently transfected reporter gene driven by the Oct-3/4 upstream region. Thus, changes in the cellular activity of trans-acting factors acting on the upstream region also contribute to the inability of the hybrid and RA-treated EC cells to generate Oct-3/4 transcripts. In conclusion, this study draws a connection between the shutdown of Oct-3/4 expression in RA-differentiated EC cells and its extinction in hybrid cells. In both systems, repression of Oct-3/4 expression is achieved through changes in the methylation status, chromatin structure, and transcriptional activity of the Oct-3/4 upstream regulatory region.

Animals↗
PubMed1999

Acquisition and extinction of somatic symptoms in response to odours: a Pavlovian paradigm relevant to multiple chemical sensitivity.

OBJECTIVES: Multiple chemical sensitivity is a poorly understood syndrome in which various symptoms are triggered by chemically unrelated, but often odorous substances, at doses below those known to be harmful. This study focuses on the process of pavlovian acquisition and extinction of somatic symptoms triggered by odours. METHODS: Diluted ammonia and butyric acid were odorous conditioned stimuli (CS). The unconditioned stimulus (US) was 7.4% CO2 enriched air. One odour (CS+) was presented together with the US for 2 minutes (CS+ trial), and the other odour (CS-) was presented with air (CS-trial). Three CS+ and three CS-exposures were run in a semi-randomised order; this as the acquisition (conditioning) phase. To test the effect of the conditioning, each subject then had one CS+ only--that is, CS+ without CO2--and one CS- test exposure. Next, half the subjects (n = 32) received five additional CS+ only exposures (extinction group), while the other half received five exposures to breathing air (wait group). Finally, all subjects got one CS+ only test exposure to test the effect of the extinction. Ventilatory responses were measured during and somatic symptoms after each exposure. RESULTS: More symptoms were reported upon exposure to CS+ only than to CS-odours, regardless of the odour type. Altered respiratory rate was only found when ammonia was CS+. Five extinction trials were sufficient to reduce the level of acquired symptoms. CONCLUSION: Subjects can acquire somatic symptoms and altered respiratory behaviour in response to harmless, but odorous chemical substances, if these odours have been associated with a physiological challenge that originally had caused these symptoms. The conditioned symptoms can subsequently be reduced in an extinction procedure. The study further supports the plausibility of a pavlovian conditioning hypothesis to explain the pathogenesis of MCS.

Adult↗
PubMed1989

Periodicity in extinction and the problem of catastrophism in the history of life.

The hypothesis that extinction events have recurred periodically over the last quarter billion years is greatly strengthened by new data on the stratigraphic ranges of marine animal genera. In the interval from the Permian to Recent, these data encompass some 13,000 generic extinctions, providing a more sensitive indicator of species-level extinctions than previously used familial data. Extinction time series computed from the generic data display nine strong peaks that are nearly uniformly spaced at 26 Ma intervals over the last 270 Ma. Most of these peaks correspond to extinction events recognized in more detailed, if limited, biostratigraphic studies. These new data weaken or negate most arguments against periodicity, which have involved criticisms of the taxonomic data base, sampling intervals, chronometric time scales, and statistical methods used in previous analyses. The criticisms are reviewed in some detail and various new calculations and simulations, including one assessing the effects of paraphyletic taxa, are presented. Although the new data strengthen the case for periodicity, they offer little new insight into the deriving mechanism behind the pattern. However, they do suggest that many of the periodic events may not have been catastrophic, occurring instead over several stratigraphic stages or substages.

Biological Evolution↗
PubMed1997

Extinction of immunoglobulin gene expression in B cells upon fusion with HeLa cells is preceded by rapid nuclear depletion of essential transcription factors and is accompanied by widespread inactivation of genes expressed in a B cell-specific manner.

When immunoglobulin (Ig) expressing B cells are fused with non-B cells, Ig expression is rapidly suppressed at the level of transcription, a phenomenon termed extinction. Here we demonstrate that fusion of HeLa cells with either diploid or tetraploid B cells (Daudi) results in widespread extinction of several other B cell-encoded genes that are expressed in a B cell-specific manner. In contrast, expression of B cell-expressed genes that are not dependent on cell-specific controls is unaffected. We show that the molecular mechanism(s) underlying Ig gene extinction can be explained, at least in part, by a lack of transcription factors that are essential for Ig gene transcription. These transcription factors are either not produced due to block of transcription of their respective genes (Oct-2, OBF-1, PU.1), or are rendered inactive posttranslationally (NF-kappa B, E47). By isolating Daudi x HeLa heterokaryons a few hours after fusion, we have studied the initial fate of two B cell-specific transcription factors involved in Ig gene transcription, Oct-2 and NF-kappa B. This report provides the first demonstration that upon fusion with HeLa cells, the nuclear contents of B cell-expressed transcription factors are depleted within a few hours with kinetics that are as fast or faster than that of Ig gene extinction. Thus, the extinguishing mechanism is effective very early after fusion. We suggest that extinction of Ig genes is part of a global mechanism that suppresses the differentiation program foreign to the HeLa phenotype.

B-Lymphocytes↗
PubMed2002

Optical and physical properties of stratospheric aerosols from balloon measurements in the visible and near-infrared domains. 1. Analysis of aerosol extinction spectra from the AMON and SALOMON balloonborne spectrometers.

Aerosol extinction coefficients have been derived in the 375-700-nm spectral domain from measurement in the stratosphere since 1992, at night, at mid- and high latitudes from 15 to 40 km, by two balloonborne spectrometers, Absorption par les Minoritaires Ozone et NO(chi) (AMON) and Spectroscopie d'Absorption Lunaire pour l'Observation des Minoritaires Ozone et NO(chi) (SALOMON). Log-normal size distributions associated with the Mie-computed extinction spectra that best fit the measurements permit calculation of integrated properties of the distributions. Although measured extinction spectra that correspond to background aerosols can be reproduced by the Mie scattering model by use of monomodal log-normal size distributions, each flight reveals some large discrepancies between measurement and theory at several altitudes. The agreement between measured and Mie-calculated extinction spectra is significantly improved by use of bimodal log-normal distributions. Nevertheless, neither monomodal nor bimodal distributions permit correct reproduction of some of the measured extinction shapes, especially for the 26 February 1997 AMON flight, which exhibited spectral behavior attributed to particles from a polar stratospheric cloud event.

Journal Article↗
PubMed2005

Particle extinction measured at ambient conditions with differential optical absorption spectroscopy. 1. system setup and characterization.

We describe an instrument for measuring the particle extinction coefficient at ambient conditions in the spectral range from 270 to 1000 nm. It is based on a differential optical absorption spectroscopy (DOAS) system, which was originally used for measuring trace-gas concentrations of atmospheric absorbers in the ultraviolet-visible wavelength range. One obtains the particle extinction spectrum by measuring the total atmospheric extinction and subtracting trace-gas absorption and Rayleigh scattering. The instrument consists of two nested Newton-type telescopes, which are simultaneously used for emitting and detecting light, and two arrays of retroreflectors at the ends of the two light paths. The design of this new instrument solves crucial problems usually encountered in the design of such instruments. The telescope is actively repositioned during the measurement cycle. Particle extinction is simultaneously measured at several wavelengths by the use of two grating spectrometers. Optical turbulence causes lateral movement of the spot of light in the receiver telescope. Monitoring of the return signals with a diode permits correction for this effect. Phase-sensitive detection efficiently suppresses background signals from the atmosphere as well as from the instrument itself. The performance of the instrument was tested during a measurement period of 3 months from January to March 2000. The instrument ran without significant interruption during that period. A mean accuracy of 0.032 km(-1) was found for the extinction coefficient for an 11-day period in March.

Journal Article↗
PubMed2006

Validation of the Raman lidar algorithm for quantifying aerosol extinction.

To calculate aerosol extinction from Raman lidar data, it is necessary to evaluate the derivative of a molecular Raman signal with respect to range. The typical approach taken in the lidar community is to make an a priori assumption about the functional behavior of the data to calculate the derivative. It has previously been shown that the use of the chi-squared technique to determine the most likely functional behavior of the data prior to actually calculating the derivative eliminates the need for making a priori assumptions. Here that technique is validated through numerical simulation and by application to a significant body of Raman lidar measurements. In general, we show that the chi-squared approach for evaluating extinction yields lower extinction uncertainty than traditional techniques. We also use the technique to study the feasibility of developing a general characterization of the extinction uncertainty that could permit the uncertainty in Raman lidar aerosol extinction measurements to be estimated accurately without the need of the chi-squared technique.

Journal Article↗
PubMed2001

On the extinction of radiation by a homogeneous but spatially correlated random medium.

Exponential extinction of incoherent radiation intensity in a random medium (sometimes referred to as the Beer-Lambert law) arises early in the development of several branches of science and underlies much of radiative transfer theory and propagation in turbid media with applications in astronomy, atmospheric science, and oceanography. We adopt a stochastic approach to exponential extinction and connect it to the underlying Poisson statistics of extinction events. We then show that when a dilute random medium is statistically homogeneous but spatially correlated, the attenuation of incoherent radiation with depth is often slower than exponential. This occurs because spatial correlations among obstacles of the medium spread out the probability distribution of photon extinction events. Therefore the probability of transmission (no extinction) is increased.

Journal Article↗
PubMed2005

Orientation-averaged light-extinction characteristics of compound particles including aggregate effects.

Orientation-averaged light-extinction characteristics of compound sulfate-carbon-soot particles have been analyzed with a discrete-dipole algorithm (DDSCAT code) for r1/r2 (ratio of primary-particle radius to secondary-particle radius) in the range 7 to 1 and for wavelengths from 0.4 to 0.8 microm. It was found that compound particles above a particle radius of approximately 0.2 microm exhibit light-extinction characteristics that closely match those of a pure sulfate particle. The shielding of the carbon particle by the primary particle apparently reduces the absorption effect of the soot particle over the range of all possible orientations. In light of the fact that soot particles tend to be small in comparison with host sulfate particles, the light-extinction characteristics of compound particles are dictated by the optical properties of the host particles. This result has been applied for aerosol aggregates with log-normal size distributions. For r1/r2 > or = 2 the aggregate extinction coefficient of a group of compound particles remains within 12% of that of a group consisting only of sulfate particles. This allows for effective calculation of the overall aerosol light extinction on the basis of the optical and geometrical properties of the constituent particles without having to include a compound-geometry effect.

Journal Article↗
PubMed2006

Forecasting extinction risk with nonstationary matrix models.

Matrix population growth models are standard tools for forecasting population change and for managing rare species, but they are less useful for predicting extinction risk in the face of changing environmental conditions. Deterministic models provide point estimates of lambda, the finite rate of increase, as well as measures of matrix sensitivity and elasticity. Stationary matrix models can be used to estimate extinction risk in a variable environment, but they assume that the matrix elements are randomly sampled from a stationary (i.e., non-changing) distribution. Here we outline a method for using nonstationary matrix models to construct realistic forecasts of population fluctuation in changing environments. Our method requires three pieces of data: (1) field estimates of transition matrix elements, (2) experimental data on the demographic responses of populations to altered environmental conditions, and (3) forecasting data on environmental drivers. These three pieces of data are combined to generate a series of sequential transition matrices that emulate a pattern of long-term change in environmental drivers. Realistic estimates of population persistence and extinction risk can be derived from stochastic permutations of such a model. We illustrate the steps of this analysis with data from two populations of Sarracenia purpurea growing in northern New England. Sarracenia purpurea is a perennial carnivorous plant that is potentially at risk of local extinction because of increased nitrogen deposition. Long-term monitoring records or models of environmental change can be used to generate time series of driver variables under different scenarios of changing environments. Both manipulative and natural experiments can be used to construct a linking function that describes how matrix parameters change as a function of the environmental driver. This synthetic modeling approach provides quantitative estimates of extinction probability that have an explicit mechanistic basis.

Adaptation, Physiological↗
PubMed1995

Prevalence of the extinction burst and its attenuation during treatment.

Although extinction has been an effective treatment for a variety of behavior disorders, its use may be associated with several adverse side effects, the most common being an initial increase in the frequency of the target response, called an "extinction burst." We attempted to determine the prevalence of the extinction burst in applied research and its possible attenuation with other operant procedures. An analysis of 113 sets of extinction data indicated that bursting may not be as common as previously assumed (it occurred in 24% of the cases) and may be less likely when extinction is implemented with alternative procedures rather than as the sole intervention (bursting was evident in 12% of the former cases and 36% of the latter).

Journal Article↗
PubMed2005

Estimation of extinction probabilities of five german cattle breeds by population viability analysis.

The estimation of the expected loss of genetic diversity and marginal diversities in a set of breeds within a defined future time horizon requires initial estimates of breed extinction probabilities. In this study, the extinction probabilities of 5 German dual-purpose cattle breeds were estimated by population viability analysis. Regression was used to estimate the infinitesimal mean and variance of the population growth and this was based on the diffusion approximation of the density independent population growth (also known as the Dennis regression model). The annual number of milk-recorded cows in each breed was used as census data. Based on the regression results, the extinction probabilities and their confidence intervals were estimated for a wide variety of future time horizons using Monte Carlo time series simulations. The estimates of extinction probabilities were sensible, but in 2 cases they depended heavily on the time horizon considered. Additionally, the confidence intervals became very wide with an increased time horizon. We recommend the estimation of extinction probabilities for a set of future time horizons rather than for a single future time and the selection of an upper bound for this set that is not too large to be meaningful. The validity of the use of the number of milk-recorded cows as census data and of the model assumptions is discussed in detail.

Animals↗
PubMedDate not supplied

[Effect of the activation of GABA A, benzodiazepine, and D2 dopamine receptors on the passive avoidance extinction in submissive and aggressive mice].

The effect of activation of GABAA, benzodiazepine, and D2 dopamine receptors on extinction of passive avoidance and their dependence on the initial state of aggressive and submissive C57BL/6J mice were studied. It was found that in mice with the submissive stereotype of behavior produced by experience of defeats in daily agonistic confrontations, extinction of the conditioned reaction occurred faster than in control mice. The activation of D2 receptors by quinpirole and of benzodiazepine receptors by medasepam before training restored the retrieval of the memory trace. A prolongation of extinction was observed in aggressive mice in comparison with control and submissive animals, and activation of GABAA by muscimol and benzodiazepine receptors by medazepam led to acceleration of extinction. Activation of D2 receptors was ineffective. Thus, the difference in initial behavioral strategy determined both the development of extinction of the passive avoidance and variability of participation of D2, GABAA, and benzodiazepine receptors in the maintenance of availability of the memory trace to retrieval.

Aggression↗
PubMed2025

Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss.

Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon-thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of a chromosomal-level genome of the extinct thylacine offers a unique opportunity for such comparative studies. Here, we leverage palaeogenomic data to compare gene presence/absence patterns between the Tasmanian devil and thylacine. We discovered ancestral (between 13-1 Ma) loss of SAMD9L, HSD17B13, CUZD1 and VWA7 due to multiple gene-inactivating mutations, corroborated by short-read sequencing. The timing of gene loss mirrors the thylacine's shift towards hypercarnivory and increased body size. Notably, the loss of SAMD9 correlates with a carnivorous diet. Our genome-wide analysis reveals olfactory receptor loss and relaxed selection, aligning with reduced olfactory lobes in the thylacine, indicating olfaction is not its primary hunting sense. By integrating palaeogenomic data with comparative genomics, our study reveals ancestral gene losses and their impact on species survival and resilience to environmental changes. Our approach can be extended to other extinct and endangered species, helping to identify genetic factors for conservation efforts.

Animals↗
PubMed1990

Ipsilateral extinction in the hemineglect syndrome.

Data suggest right-hemisphere dominance for attention. Right-hemisphere lesions reduce attentional capacity that may manifest as neglect or extinction. Attention can be assessed with the Face-Hand Test where touch on the face may extinguish simultaneous touch on the hand. Extinction ipsilateral to unilateral lesions suggests abnormal attention to ipsilateral hemispace. We tested patients with left- and right-hemisphere lesions without neglect and right-hemisphere lesions with neglect with stimuli applied exclusively ipsilateral to lesions. In experiment 1, stimuli were applied in face-hand combinations. In experiment 2, the Face-Hand Test was ranked from 0 (no extinction) to 7 (marked extinction) using progressively greater stimulation. In both experiments, right-hemisphere patients with neglect made significantly more errors than left-hemisphere patients without neglect. These data support models of bidirectional right-hemisphere attentional dominance.

Attention↗
PubMed2006

Ventral hippocampal muscimol disrupts context-specific fear memory retrieval after extinction in rats.

Research aimed at understanding Pavlovian fear memory extinction has yielded considerable insight into the conditions under which fear memories may become inhibited. After extinction, Pavlovian fear memory retrieval is context-specific. Fear memories are not expressed in the extinction context, but they are expressed in every other context. Research indicates that the dorsal hippocampus mediates the context-specific expression of fear memory, but the role of the ventral hippocampus in mediating this process is unknown. Insofar as the ventral hippocampus is involved in the acquisition and expression of both context and tone fear, we asked whether GABA systems in the ventral hippocampus mediate context-specific fear memory retrieval after extinction. Experiment 1 showed that ventral hippocampal inactivation with muscimol disrupted context-specific fear memory retrieval. Experiment 2 showed that rats infused with muscimol can discriminate a context in which they were shocked from a neutral context. Nonetheless, they do appear to have a mild impairment in this task. Experiment 3 showed that ventral hippocampal muscimol did not disrupt locomotor activity, but did result in a slight increase in freezing and grooming, an effect that cannot explain the context-specific retrieval deficit demonstrated in experiment 1. These data are consistent with a role for the ventral hippocampus in mediating context-specific fear memory retrieval.

Animals↗
PubMed1980

The effects of hippocampectomy and of fimbria section upon the partial reinforcement extinction effect in rats.

Rats were trained to run in an alley for food reward given on every trial (continuous reinforcement, CR) or on a random 50% of trials (partial reinforcement, PR) and were then extinguished. Sham-operated controls showed the usual partial reinforcement extinction effect (PREE), i.e., PR-trained animals were more resistant to extinction than CR-trained animals. The PREE was abolished by hippocampectomy, which increased resistance to extinction in CR-trained rats and decreased it in PR-trained rats. Bilateral fimbria section had no effect on resistance to extinction in either condition. These results are discussed in the light of theories of hippocampal function and the anatomy of septohippocampal connections.

Animals↗