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PubMed1997

Adaptation and extinction in changing environments.

The extinction risk of a population is determined by its demographic properties, the environmental conditions to which it is exposed, and its genetic potential to cope with and adapt to its environment. All these factors may have stochastic as well as directional components. The present chapter reviews several types of models concerned with the vulnerability of small populations to demographic stochasticity and to random and directional changes of the environment. In particular, the influence of mutation and genetic variability on the persistence time of a population is explored, critical rates for environmental change are estimated beyond which extinction on time scales of tens to a few thousand generations is virtually certain, and the extinction risks caused by the above mentioned factors are compared.

Adaptation, Physiological↗

PubMed1980

The extinction of slowly evolving dynamical systems.

The time evolution of slowly evolving discrete dynamical systems xi + 1 = T(ri, xi), defined on an interval [0, L], where a parameter ri changes slowly with respect to i is considered. For certain transformations T, once ri reaches a critical value the system faces a non-zero probability of extinction because some xj psi [0, L]. Recent ergodic theory results of Ruelle, Pianigiani, and Lasota and Yorke are used to derive a simple expression for the probability of survival of these systems. The extinction process is illustrated with two examples. One is the quadratic map, T (r, x) = rx (1 - x), and the second is a simple model for the growth of a cellular population. The survival statistics for chronic myelogenous leukemia patients are discussed in light of these extinction processes. Two other dynamical processes of biological importance, to which our results are applicable, are mentioned.

Biological Evolution↗

PubMed1975

Extinction of liver-specific functions in hybrids between differentiated and dedifferentiated rat hepatoma cells.

A cross has been performed between dedifferentiated rat hepatoma cells and the differentiated cells from which they were derived. 10 hybrid clones, containing the complete chromosome sets of both parents, show extinction of 4 liver-specific enzymes: tyrosine aminotransferase (E.C. 2.6.1.5), alanine aminotransferase (E.C. 2.6.1.2), and the liver-specific isozymes of alcohol dehydrogenase (E.C. 1.1.1.1) and aldolase (E.C. 4.1.2.13). Moreover, the 4 hybrid clones examined do not produce albumin . The only function of the differentiated parent which is not extinguished in the hybrid cells is inducibility of the aminotransferases. For 3 of the hybrid clones, extinction of 3 of the 4 enzymes is incomplete, but these clones do not differ in modal chromosome number from those which show more complete extinction of the enzymes. Subcloning of several of the hybrids revealed that the phenotype of the hybrids is very stable; 4 subclones showing reexpression of intermediate levels of the enzymes are characterized. These results show that dedifferentiation of the parental cells is not due to the simple loss of some factor required for the maintenance of expression of differentiated functions, and suggest that dedifferentiation is due to the activation of some control mechanism, whose final effect is negative, and which may be a part of the epigenotype of the embryonic hepatocyte.

Alanine Transaminase↗

PubMed1996

Characterization of somatic cell hybrids exhibiting extinction of AFP, albumin and an AFP-HPRT transgene.

We utilized an AFP-HPRT transgene, i.e. the HPRT coding sequences under the regulation of AFP enhancer and promoter sequences, to localize the AFP extinguisher locus in intertypic somatic cell hybrids (hepatoma X fibroblast). This hybrid gene construct, which directly links AFP regulation to a reversibly selective gene, enabled the selection of stably transfected cells which express AFP, as well as cells showing extinction of AFP. Mouse hepatoma cells stably transfected with and expressing the transgene were fused to human fibroblasts, and the resulting somatic cell hybrids were characterized using Southern, Northern and karyotypic analyses. That several hybrids exhibited the proper extinction of AFP, AFP-HPRT and albumin suggests coregulation of these genes by an extinguisher. Segregant lines derived from these hybrids were selected for the loss of extinguisher activity and for reexpression of the transgene. Karyotypic analysis of hybrid and segregant lines, exhibiting proper AFP, albumin and AFP-HPRT phenotypes, revealed that the presence of human chromosome 7 was most closely associated with the AFP-extinguished state. The hybrids generated in these studies now make it possible to isolate the sequences responsible for AFP and albumin extinction.

Albumins↗

PubMed2005

Extinction may not be forever.

Here we review the phenomenon of ecomorph evolution and the hypothesis of iterative climatic cycles. Although a widely known phenomenon, convergent evolution has been underappreciated in both its scope and commonality. The power of natural selection to override genealogy to create similar morphologies (even among distantly related organisms) supports classical Darwinian evolution. That this occurs repeatedly in stratigraphically closely spaced intervals is one of the most striking features of Earth history. Periodic extinctions followed by re-evolution of adaptive types (ecomorphs) are not isolated occurrences but are embedded within complex ecological systems that evolve, become extinct, and repeat themselves in temporal synchrony. These complexes of radiation and extinction bundle the biostratigraphic record and provide the basis for a global stratigraphy. At this scale, climatic change is the only mechanism adequate to explain the observed record of repeating faunas and floras. Understanding of the underlying causes may lead to predictive theories of global biostratigraphy, evolutionary processes, and climatic change.

Animals↗

PubMed2003

Local species immigration, extinction, and turnover of butterflies in relation to habitat area and habitat isolation.

Temporal dynamics of insect communities in terrestrial habitat fragments have been rarely studied. Here it was tested whether immigration, extinction, and turnover of butterfly species change with area and isolation of 31 calcareous grasslands. The area ranged from 0.03 to 5.14 ha, the isolation index from 2,100 to 86,000 (edge-to-edge distance 55-1,894 m). In both study years (1996, 2000), the total number of individuals (16,466, 15,101) and species (60, 54) sampled across all sites were similar and number of species increased with area in both years indicating an equilibrium. Rates of extinction (38% for habitat specialists vs. 20% for generalists) and turnover (51% vs. 35%) were higher, and rates of immigration (11% vs. 30%) were lower for habitat specialists than for generalists. Extinction and turnover rates decreased with increasing fragment size for both specialist ( n=25 species) and generalist ( n=36) butterflies, but specialists showed a significantly steeper decrease with increasing fragment size than generalists. Immigration rates increased with area. As a result, species number of habitat specialists declined in small habitats but not in large habitats between 1996 and 2000. No significant impact of habitat isolation on the butterfly community was found. The data suggest that large habitat fragments are of special importance for the conservation of the specialized, most endangered butterfly species. Habitat isolation appears to be less important, as butterflies can cope with the habitat mosaic in our study region.

Animals↗

PubMed1989

Calculation of protein extinction coefficients from amino acid sequence data.

Quantitative study of protein-protein and protein-ligand interactions in solution requires accurate determination of protein concentration. Often, for proteins available only in "molecular biological" amounts, it is difficult or impossible to make an accurate experimental measurement of the molar extinction coefficient of the protein. Yet without a reliable value of this parameter, one cannot determine protein concentrations by the usual uv spectroscopic means. Fortunately, knowledge of amino acid residue sequence and promoter molecular weight (and thus also of amino acid composition) is generally available through the DNA sequence, which is usually accurately known for most such proteins. In this paper we present a method for calculating accurate (to +/- 5% in most cases) molar extinction coefficients for proteins at 280 nm, simply from knowledge of the amino acid composition. The method is calibrated against 18 "normal" globular proteins whose molar extinction coefficients are accurately known, and the assumptions underlying the method, as well as its limitations, are discussed.

Amino Acid Sequence↗

PubMed1989

Opiate antagonists and self-stimulation: extinction-like response patterns suggest selective reward deficit.

The present study investigated the response decrement patterns produced by opiate antagonists on intracranial self-stimulation behavior, in order to determine if these drugs affect the reinforcement value of the stimulation or interfere with the ability of the animal to respond. Male rats lever-pressed in 60-min sessions on a continuous reinforcement schedule for self-stimulation of the nucleus accumbens. Naloxone (2.0 and 20 mg/kg) and naltrexone (2.0 and 20 mg/kg) suppressed self-stimulation only after a significant delay, in an extinction-like response decrement pattern, mimicking the effects of reductions in current intensity (75% and 50% of baseline). The increasing behavioral effects characteristic of the extinction pattern were observed despite the fact that testing began after the time point at which maximal suppression of self-stimulation occurs with these drugs, and when brain concentrations of these drugs were declining. Since normal responding was observed for several minutes after the beginning of the session, the results may explain why long sessions are necessary to observe suppression of self-stimulation by opiate antagonists. The extinction-like pattern produced by these drugs suggests that opiate antagonists suppress self-stimulation by reducing the reinforcement value of the stimulation, rather than by interfering with the ability of the animal to respond. These findings are consistent with a role for endogenous opioid peptides in brain stimulation reward.

Animals↗

PubMed1987

Gonadal steroids and the extinction of conditioned taste aversions in young domestic fowl.

Three experiments using domestic chicks demonstrate that the extinction of a conditioned taste aversion to a green-coloured sucrose solution is slowed by the administration of testosterone or 5 alpha-dihydrotestosterone but is unaffected by estradiol. Testosterone slows extinction in male and female chicks to an equal extent. Previously described effects of testosterone on attentional and memory mechanisms have also been produced by low doses of estradiol so a separate mechanism must be postulated to explain the present results. It is probably similar to the mechanism responsible for a steroid-dependent slowing of extinction in rats since those effects are also androgenic and present in both sexes.

Animals↗

PubMed1990

Extinction of an immunoglobulin kappa promoter in cell hybrids is mediated by the octamer motif and correlates with suppression of Oct-2 expression.

When immunoglobulin-expressing B cells are fused with fibroblasts, immunoglobulin expression is rapidly and selectively suppressed. here we demonstrate that the conserved octamer motif of a kappa light chain gene promoter plays a crucial role in mediating this "extinction" phenomenon. Replacement of this octamer site by an Sp1 or NF1 binding site is sufficient to bypass extinction. Furthermore, in early cell hybrids, immunoglobulin suppression is correlated with absence of the cell-specific transcription factor Oct-2 and its transcripts. Such hybrids cannot support transcription of a transiently introduced reporter plasmid, driven by an octamer-containing promoter, unless an expression vector encoding Oct-2 is cotransfected. Transfection of the same Oct-2 expression vector into hybrid cells is also sufficient to "reactivate" an integrated kappa promoter construct. Thus, our data further establish the role of Oct-2 for immunoglobulin transcription and show that in B cell x fibroblast hybrids, the lack of a necessary cell-specific transcription factor is involved in the extinction of immunoglobulin expression.

Animals↗

PubMed1983

Solution composition dependent variation in extinction coefficients for p-nitroaniline.

The dependence of the extinction coefficients for para-nitroaniline on solution composition has been investigated. The p-nitroaniline absorption spectrum is red-shifted with increasing ionic strength, with the consequence that the extinction coefficients at fixed wavelengths may vary significantly. The isosbestic wavelength for peptide p-nitroanilide/p-nitroaniline mixtures is similarly shifted. Poly(ethylene glycol) and bovine albumin, two additives frequently employed to eliminate enzyme loss from adsorption to cuvette and dilution vessel surfaces, also induce shifts in the p-nitroaniline spectrum. The use of a difference extinction coefficient at 381 nm, the p-nitroaniline maximum wavelength, is proposed to minimize the error resulting from solution composition dependent spectral shifts.

Aniline Compounds↗

PubMed1990

Conditioned diastolic blood pressure: the effects of magnitude of acquired response and feedback schedules on resistance to extinction.

The purpose of this experiment was to examine the effects of: (a) training to two different response magnitude criteria, and (b) three different feedback schedules on the acquisition and subsequent extinction of diastolic blood pressure changes. Subjects were 20 male and female normotensive volunteer college students, ages 18-36 years. A 3 x 2 design was used in which 3 schedules of reinforcement (0, 50 and 100%) were factorially compared with two response magnitude training criteria (10% and 20% of resting basal diastolic blood pressure). The results indicated that while the partial reinforcement effect appears to hold for the acquisition of bidirectional diastolic blood pressure changes, different response magnitude training criteria seemed to have a greater influence in producing significant differences in acquisition rate during the training of diastolic blood pressure decreases. Resistance to extinction was notably weak across all conditions, with most subjects failing to exhibit previously acquired bidirectional diastolic blood pressure performance after the end of the first extinction session.

Adolescent↗

PubMedDate not supplied

Albumin extinction followed by de novo methylation of its gene in somatic hybrids of a rat hepatoma.

We have previously identified an Msp I site at the 5' end of the rat albumin gene whose undermethylation is necessary but not sufficient for stable albumin expression in rat hepatoma cells. We have also shown that the extinction of albumin expression in somatic hybrids is not the result of methylation at this site, since for two different crosses, rapid extinction was found to occur in the absence of any de novo methylation of the previously active gene. In the present study, we examine albumin expression and albumin gene methylation for independent hybrid clones isolated from crosses between albumin expressing rat hepatoma cells and cells of two different non-expressing lines. The cells from hybrid clones of both crosses are characterized by stable extinction of albumin expression. Moreover, we find that de novo methylation of the "extinguished" albumin gene can occur in somatic hybrids, but only some weeks after the gene has ceased to be expressed.

Animals↗

PubMed2004

Reductive titration of photosystem I and differential extinction coefficient of P700+ at 810-950 nm in leaves.

We describe a method of reductive titration of photosystem I (PSI) density in leaves by generating a known amount of electrons (e-) in photosystem II (PSII) and measuring the resulting change in optical signal as these electrons arrive at pre-oxidized PSI. The method complements a recently published method of oxidative titration of PSI donor side e- carriers P700, plastocyanin (PC) and cytochrome f by illuminating a darkened leaf with far-red light (FRL) [V. Oja, H. Eichelmann, R.B. Peterson, B. Rasulov, A. Laisk, Decyphering the 820 nm signal: redox state of donor side and quantum yield of photosystem I in leaves, Photosynth. Res. 78 (2003) 1-15], presenting a nondestructive way for the determination of PSI density in intact leaves. Experiments were carried out on leaves of birch (Betula pendula Roth) and several other species grown outdoors. Single-turnover flashes of different quantum dose were applied to leaves illuminated with FRL, and the FRL was shuttered off immediately after the flash. The number of e- generated in PSII by the flash was measured as four times O2 evolution following the flash. Reduction of the pre-oxidized P700 and PC was followed as a change in leaf transmittance using a dual-wavelength detector ED P700DW (810 minus 950 nm, H. Walz, Effeltrich, Germany). The ED P700DW signal was deconvoluted into P700+ and PC+ components using the abovementioned oxidative titration method. The P700+ component was related to the absolute number of e- that reduced the P700+ to calculate the extinction coefficient. The effective differential extinction coefficient of P700+ at 810-950 nm was 0.40+/-0.06 (S.D.)% of transmittance change per micromol P700+ m(-2) or 17.6+/-2.4 mM(-1) cm(-1). The result shows that the scattering medium of the leaf effectively increases the extinction coefficient by about two times and its variation (+/-14% S.D.) is mainly caused by light-scattering properties of the leaf.

Light↗

PubMed2005

Unexpected amino acid composition of modern Reptilia and its implications in molecular mechanisms of dinosaur extinction.

Dinosaur extinction is a great challenge to evolutionary biology. Although accumulating evidence suggests that an abrupt change of environment, such as a long period of low temperature induced by asteroid hit or other disasters, may be responsible for dinosaur extinction, little is known about the underlying molecular mechanisms. By analyzing the amino acid compositions of 13 biological classes, we found that the charged amino acid content of modern Reptilia, the sibling of dinosaur, is strikingly different from those of other classes, which inspires us to propose a possible molecular mechanism for dinosaur extinction.

Amino Acid Sequence↗

PubMed2004

Extinction times and moment closure in the stochastic logistic process.

We investigate the statistics of extinction times for an isolated population, with an initially modest number M of individuals, whose dynamics are controlled by a stochastic logistic process (SLP). The coefficient of variation in the extinction time V is found to have a maximum value when the death and birth rates are close in value. For large habitat size K we find that Vmax is of order K1/4 / M1/2, which is much larger than unity so long as M is small compared to K1/2. We also present a study of the SLP using the moment closure approximation (MCA), and discuss the successes and failures of this method. Regarding the former, the MCA yields a steady-state distribution for the population when the death rate is low. Although not correct for the SLP model, the first three moments of this distribution coincide with those calculated exactly for an adjusted SLP in which extinction is forbidden. These exact calculations also pinpoint the breakdown of the MCA as the death rate is increased.

Animals↗

PubMed2005

Quasispecies dynamics and RNA virus extinction.

The extinction of foot-and-mouth disease virus (FMDV) is strongly influenced by mutation rates, types of mutations, relative viral fitness and virus population regimens during infection. Here we review experimental results and theoretical models that describe a contrast between the effective extinction of FMDV subjected to increased mutagenesis, and the remarkable resistance to extinction of the same and related FMDV clones subjected to serial bottleneck events. The results suggest procedures to master key parameters to develop effective antiviral strategies based on virus entry into error catastrophe.

Animals↗

PubMedDate not supplied

Population extinction and recolonization in human demographic history.

For over 30 years, a debate has raged among anthropologists about the origins of anatomically modern humans. At first the debate centered on fossil evidence, but in the past 10-15 years population geneticists have entered the fray. One model, the multiregional evolution model, posits a gradual transition from Homo erectus to anatomically modern humans throughout the Old World. In contrast, the recent African origin model hypothesizes that anatomically modern humans arose from a small, isolated population in Africa, spread out of Africa, and replaced indigenous H. erectus populations in Eurasia and Australasia. A primary objection, from a population genetics perspective, to the multiregional model is that the genetic data suggest a small effective population size for humans. This effective size is on the order of 10,000. Effective population size has a complex relationship with census size, but it has been argued that, assuming that effective size is roughly equal to the number of breeding individuals in human populations under standard demographic conditions, 10,000 breeding individuals could not have occupied much of the Old World throughout the Pleistocene and remained a cohesive species via gene flow. However, this argument is not valid if one considers population extinction and recolonization, which might have played an important role in human history during the Pleistocene. With population extinction and recolonization, the inbreeding effective population size can be small and the census size extremely large. In this paper, I will show that under conditions of population extinction and recolonization, an effective population size of 10,000 suggested by genetic data is compatible with a large census size consistent with the multiregional model.

Animals↗