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PubMed1991

Expression and characterization of recombinant human ciliary neurotrophic factor from Escherichia coli.

The gene for ciliary neurotrophic factor (CNTF) was cloned from a human genomic DNA library by screening with a DNA fragment amplified from human genomic DNA using the polymerase chain reaction. A DNA sequence coding for human CNTF was placed under control of an regulatable promoter in the expression vector pJU1003 and transformed into Escherichia coli strain BL21(DE3). Induction of expression in cultures of this transformant led to the accumulation of approx. 25 mg/l per A600 unit of human CNTF. CNTF was purified to homogeneity from cell lysates via anion-exchange, cation-exchange and Zn(2+)-affinity chromatography. Purified CNTF contained less than 0.1% contaminating E. coli proteins, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis and reversed-phase high-pressure liquid chromatography (HPLC). The protein exhibited an ultraviolet absorption maximum at 279 nm with a calculated extinction coefficient of A1%(279) = 9.0. Peptide map and amino acid sequence analyses confirmed that the expressed protein has the amino acid sequence expected for human CNTF, except for the absence of the amino-terminal methionine. High-purified recombinant human CNTF supported the survival of chick embryo parasympathetic, sympathetic and sensory neurons in culture at low picomolar concentrations. These results indicate that the biological activities previously ascribed to impure CNTF preparations indeed reside in one molecule.

Amino Acid Sequence↗

PubMed1998

Photochromic polypeptides as synthetic models of biological photoreceptors: a spectroscopic study.

L-Glutamic acid polypeptides containing photochromic nitrospiropyran bound to the side chains at various percentages ("local" concentration) have been synthesized and investigated as possible artificial models of biological photoreceptors. Absorption and fluorescence spectroscopy have been utilized to investigate the photophysical and photochemical properties of nitrospiropyrans, both inserted in the polypeptide chain and in solution as "free" dye. Conformational variations produced by dark storage and light exposure of the photochromic polypeptides have been studied by means of circular dichroism. Dark-kept "free" dyes in hexafluoro-2-propanol solution in the merocyanine form ("open" form) give rise to molecular aggregates, which have been characterized as merocyanine dimers. The equilibrium constant between the monomer and the dimer, K, and their molar extinction coefficients, epsilon, at several wavelengths have been determined. Fluorescence measurements on "free" and polypeptide-bound nitrospiropyrans suggest that the dimerization process between merocyanines is favored when the photochromic units are inserted in the polypeptide chain and that under these conditions an efficient energy transfer from the monomer (donor) to the dimer (acceptor) occurs. By varying "local" as well as total nitrospiropyran concentration, it has been shown that the dimeric species result from intermolecular interactions between photochromic groups inserted in the same polypeptide chain. The alpha-helix --> random coil transition of the polypeptide structure after dark storage has eventually been shown to be the result of the dimerization process and not of the dark isomerization per se from the "closed" spiropyran form to the "open" merocyanine form of the dye.

Circular Dichroism↗

PubMed1996

Paleobiology, community ecology, and scales of ecological pattern.

The fossil record provides a wealth of data on the role of regional processes and historical events in shaping biological communities over a variety of time scales. The Quaternary record with its evidence of repeated climatic change shows that both terrestrial and marine species shifted independently rather than as cohesive assemblages over scales of thousands of years. Larger scale patterns also show a strong individualistic component to taxon dynamics; assemblage stability, when it occurs, is difficult to separate from shared responses to low rates of environmental change. Nevertheless, the fossil record does suggest that some biotic interactions influence large-scale ecological and evolutionary patterns, albeit in more diffuse and protracted fashions than those generally studied by community ecologists. These include: (1) the resistance by incumbents to the establishment of new or invading taxa, with episodes of explosive diversification often appearing contingent on the removal of incumbents at extinction events; (2) steady states of within-habitat and global diversity at longer time scales (10(7)-l0(8) yr), despite enormous turnover of taxa; and (3) morphological and biogeographic responses to increased intensities of predation and substratum disturbance over similarly long time scales. The behavior of species and communities over the array of temporal and spatial scales in the fossil record takes on additional significance for framing conservation strategies, and for understanding recovery of species, lineages, and communities from environmental changes.

Animals↗

PubMed2002

Evolutionary suicide and evolution of dispersal in structured metapopulations.

We study the evolution of dispersal in a structured metapopulation model. The metapopulation consists of a large (infinite) number of local populations living in patches of habitable environment. Dispersal between patches is modelled by a disperser pool and individuals in transit between patches are exposed to a risk of mortality. Occasionally, local catastrophes eradicate a local population: all individuals in the affected patch die, yet the patch remains habitable. We prove that, in the absence of catastrophes, the strategy not to migrate is evolutionarily stable. Under a given set of environmental conditions, a metapopulation may be viable and yet selection may favor dispersal rates that drive the metapopulation to extinction. This phenomenon is known as evolutionary suicide. We show that in our model evolutionary suicide can occur for catastrophe rates that increase with decreasing local population size. Evolutionary suicide can also happen for constant catastrophe rates, if local growth within patches shows an Allee effect. We study the evolutionary bifurcation towards evolutionary suicide and show that a discontinuous transition to extinction is a necessary condition for evolutionary suicide to occur. In other words, if population size smoothly approaches zero at a boundary of viability in parameter space, this boundary is evolutionarily repelling and no suicide can occur.

Adaptation, Biological↗

PubMed2005

Evolutionary suicide.

The great majority of species that lived on this earth have gone extinct. These extinctions are often explained by invoking changes in the environment, to which the species has been unable to adapt. Evolutionary suicide is an alternative explanation to such extinctions. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist. In this paper different models, where evolutionary suicide occurs are discussed, and the theory behind the phenomenon is reviewed.

Adaptation, Biological↗

PubMed2006

A delayed prey-predator system with parasitic infection.

This paper analyzes a prey-predator system in which some members of the prey population and all predators are subjected to infection by a parasite. The predator functional response is a function of a weighted sum of prey abundances. Persistence and extinction criteria are derived. The stability of the interior equilibrium point is discussed. The role of delay is also addressed. Lastly the results are verified through computer simulation. Numerical simulation suggests that the delay has a destabilizing effect.

Animals↗

PubMed2004

Patterns of resource use in early Homo and Paranthropus.

Conventional wisdom concerning the extinction of Paranthropus suggests that these species developed highly derived morphologies as a consequence of specializing on a diet consisting of hard and/or low-quality food items. It goes on to suggest that these species were so specialized or stenotopic that they were unable to adapt to changing environments in the period following 1.5 Ma. The same conventional wisdom proposes that early Homo species responded very differently to the same environmental challenges. Instead of narrowing their niche it was the dietary and behavioral flexibility (eurytopy) exhibited by early Homo that enabled that lineage to persist. We investigate whether evidence taken across eleven criteria supports a null hypothesis in which Paranthropus is more stenotopic than early Homo. In six instances (most categories of direct evidence of dietary breadth, species diversity, species duration, susceptibility to dispersal, dispersal direction, and non-dietary adaptations) the evidence is inconsistent with the hypothesis. Only one line of indirect evidence for dietary breadth-occlusal morphology-is unambiguously consistent with the null hypothesis that Paranthropus' ability to process tough, fibrous food items (e.g., leaves) was reduced relative to early Homo. Other criteria (habitat preference, population density, direct and indirect evidence of dietary breadth related to incisor use) are only consistent with the hypothesis under certain conditions. If those conditions are not met, then the evidence is either inconsistent with the hypothesis, or ambiguous. On balance, Paranthropus and early Homo were both likely to have been ecological generalists. These data are inconsistent with the conventional wisdom that stenotopy was a major contributing factor in the extinction of the Paranthropus clade. Researchers will need to explore other avenues of research in order to generate testable hypotheses about the demise of Paranthropus. Ecological models that may explain the evolution of eurytopy in early hominins are discussed.

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↗

PubMed2000

A mathematical model of cancer treatment by immunotherapy.

In this paper, a detailed mathematical study of cancer immunotherapy will be presented. General principles of cancer immunotherapy and the model equations and hypotheses will be discussed. Mathematical analyses of the model equations with regard to dissipativity, boundedness of solutions, invariance of non-negativity, nature of equilibria, persistence, extinction and global stability will be analyzed. It will also be shown that bifurcations can occur, and criteria for total cure will also be derived.

Brain Neoplasms↗

PubMed2006

Gold and silver nanoparticles in sensing and imaging: sensitivity of plasmon response to size, shape, and metal composition.

Plasmonic metal nanoparticles have great potential for chemical and biological sensor applications, due to their sensitive spectral response to the local environment of the nanoparticle surface and ease of monitoring the light signal due to their strong scattering or absorption. In this work, we investigated the dependence of the sensitivity of the surface plasmon resonance (frequency and bandwidth) response to changes in their surrounding environment and the relative contribution of optical scattering to the total extinction, on the size and shape of nanorods and the type of metal, that is, Au vs Ag. Theoretical consideration on the surface plasmon resonance condition revealed that the spectral sensitivity, defined as the relative shift in resonance wavelength with respect to the refractive index change of surrounding materials, has two controlling factors: first the bulk plasma wavelength, a property dependent on the metal type, and second on the aspect ratio of the nanorods which is a geometrical parameter. It is found that the sensitivity is linearly proportional to both these factors. To quantitatively examine the dependence of the spectral sensitivity on the nanorod metal composition and the aspect ratio, the discrete dipole approximation method was used for the calculation of optical spectra of Ag-Au alloy metal nanorods as a function of Ag concentration. It is observed that the sensitivity does not depend on the type of the metal but depends largely on the aspect ratio of nanorods. The direct dependence of the sensitivity on the aspect ratio becomes more prominent as the size of nanorods becomes larger. However, the use of larger nanoparticles may induce an excessive broadening of the resonance spectrum due to an increase in the contribution of multipolar excitations. This restricts the sensing resolution. The insensitivity of the plasmon response to the metal composition is attributable to the fact that the bulk plasma frequency of the metal, which determines the spectral dispersion of the real dielectric function of metals and the surface plasmon resonance condition, has a similar value for the noble metals. On the other hand, nanorods with higher Ag concentration show a great enhancement in magnitude and sharpness of the plasmon resonance band, which gives better sensing resolution despite similar plasmon response. Furthermore, Ag nanorods have an additional advantage as better scatterers compared with Au nanorods of the same size.

Alloys↗

PubMed2005

Experimental evolution of conflict mediation between genomes.

Transitions to new levels of biological complexity often require cooperation among component individuals, but individual selection among those components may favor a selfishness that thwarts the evolution of cooperation. Biological systems with elements of cooperation and conflict are especially challenging to understand because the very direction of evolution is indeterminate and cannot be predicted without knowing which types of selfish mutations and interactions can arise. Here, we investigated the evolution of two bacteriophages (f1 and IKe) experimentally forced to obey a life cycle with elements of cooperation and conflict, whose outcome could have ranged from extinction of the population (due to selection of selfish elements) to extreme cooperation. Our results show the de novo evolution of a conflict mediation system that facilitates cooperation. Specifically, the two phages evolved to copackage their genomes into one protein coat, ensuring cotransmission with each other and virtually eliminating conflict. Thereafter, IKe evolved such extreme genome reduction that it lost the ability to make its own virions independent of f1. Our results parallel a variety of conflict mediation mechanisms existing in nature: evolution of reduced genomes in symbionts, cotransmission of partners, and obligate coexistence between cooperating species.

Bacteriophages↗

PubMed2005

Prolonged coexistence of humans and megafauna in Pleistocene Australia.

Recent claims for continent wide disappearance of megafauna at 46.5 thousand calendar years ago (ka) in Australia have been used to support a "blitzkrieg" model, which explains extinctions as the result of rapid overkill by human colonizers. A number of key sites with megafauna remains that significantly postdate 46.5 ka have been excluded from consideration because of questions regarding their stratigraphic integrity. Of these sites, Cuddie Springs is the only locality in Australia where megafauna and cultural remains are found together in sequential stratigraphic horizons, dated from 36-30 ka. Verifying the stratigraphic associations found here would effectively refute the rapid-overkill model and necessitate reconsideration of the regional impacts of global climatic change on megafauna and humans in the lead up to the last glacial maximum. Here, we present geochemical evidence that demonstrates the coexistence of humans and now-extinct megafaunal species on the Australian continent for a minimum of 15 ka.

Analysis of Variance↗

PubMed1984

Periodicity of extinctions in the geologic past.

The temporal distribution of the major extinctions over the past 250 million years has been investigated statistically using various forms of time series analysis. The analyzed record is based on variation in extinction intensity for fossil families of marine vertebrates, invertebrates, and protozoans and contains 12 extinction events. The 12 events show a statistically significant periodicity (P less than 0.01) with a mean interval between events of 26 million years. Two of the events coincide with extinctions that have been previously linked to meteorite impacts (terminal Cretaceous and Late Eocene). Although the causes of the periodicity are unknown, it is possible that they are related to extraterrestrial forces (solar, solar system, or galactic).

Animals↗

PubMed2006

Steroids, triterpenoids and molecular oxygen.

There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.

Amino Acid Sequence↗

PubMed2006

Significance of sighting rate in inferring extinction and threat.

We are now entering a time of immense environmental upheaval in which, increasingly, experts are required to provide conservation assessments. Quantitative assessment of trends in species' range and abundance is costly, requiring extensive field studies over a long period of time. Unfortunately, many species are only known through a few "chance" sightings or a handful of specimens, and therefore extinction may be even harder to ascertain. Several methods have been proposed for estimating the probability of extinction. However comparison within and between species is difficult because of variations in sighting rates. We applied a probabilistic method that incorporates sighting rate to the sighting record of Vietnamese slipper orchids (Paphiopedilum). The method generates a probability that another sighting will occur given the previous sighting rate and the time since last observation. This allows greater comparability between species discovered at different times. Its predictions were more highly correlated with the World Conservation Union criteria than previous methods. Trends in data collection and the political climate of a country, which affects access to material, are important potential sources of variation that affect sighting rates. A lack of understanding of the process by which data are generated makes inferring extinction from sighting records difficult because extinction status depends on how the sighting rate varies. However such methods allow rapid conservation prioritization of taxa that are poorly known and would otherwise go unassessed.

Conservation of Natural Resources↗

PubMed1998

Decoupled temporal patterns of evolution and ecology in two post-Paleozoic clades.

Counts of taxonomic diversity are the prevailing standards for documenting large-scale patterns of evolution in the fossil record. However, the secular pattern of relative ecological importance between the bryozoan clades Cyclostomata and Cheilostomata is not reflected fully in compilations of generic diversity or within-fauna species richness, and the delayed ecological recovery of the Cheilostomata after the mass extinction at the Cretaceous-Tertiary boundary is missed entirely. These observations demonstrate that evolutionary success and ecological dominance can be decoupled and profoundly different, even over tens of millions of years.

Animals↗

PubMed2005

Homosexual signification: a moral construct in social contexts.

Contemporary attempts to define homophobia argue that it is a composite prejudice reflecting attitudes toward masculinity, sexual license, and social norms. Influenced by studies of other forms of prejudice, researchers have focused on trying to identify characteristics of a "homophobic personality". Strategies to reduce homophobia emphasize education and tolerance. There has yet to be an engaged, respectful discussion of the validity of the fears which constitute the phobia in homophobia. This paper suggests a taxonomy of moral themes which recur in arguments against homosexuality. Judeo-Christian writers quote the scriptural proscription of male anal intercourse and the particularly Christian notion of homosexuality as sin (although it is but one particular in a general denunciation of all non-reproductive sexual acts). Secular concern with masculinity, sex and gender role conformity is also a source of homophobic angst. The contention that homosexual acts are against nature is premised on the biological imperative toward reproduction of the species. It does not address the possibility that human sexuality may have other ends and it certainly is not against an individual nature. Clerical and civic authority exist to maintain social order and to restrain individual license and that to justify the establishment of a normative sexuality. Among marginalized groups, the practice of exclusive homosexuality may provoke fears of ethnic extinction. Lastly, homosexuality has a history associated with social evils, debauchery, prostitution, criminality and pathology. That heritage still affects the desirability or fear of identification as a homosexual or association with homosexuals. It is my intent that this paper will contribute to understanding the etiology of antagonistic attitudes toward homosexuality and promote an overdue acceptance.

Christianity↗

PubMed2001

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Adaptation, Biological↗