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PubMed2004

Competition and natural selection in a mathematical model of cancer.

A malignant tumor is a dynamic amalgamation of various cell phenotypes, both cancerous (parenchyma) and healthy (stroma). These diverse cells compete over resources as well as cooperate to maintain tumor viability. Therefore, tumors are both an ecological community and an integrated tissue. An understanding of how natural selection operates in this unique ecological context should expose unappreciated vulnerabilities shared by all cancers. In this study I address natural selection's role in tumor evolution by developing and exploring a mathematical model of a heterogenous primary neoplasm. The model is a system of nonlinear ordinary differential equations tracking the mass of up to two different parenchyma cell types, the mass of vascular endothelial cells from which new tumor blood vessels are built and the total length of tumor microvessels. Results predict the possibility of a hypertumor-a focus of aggressively reproducing parenchyma cells that invade and destroy part or all of the tumor, perhaps before it becomes a clinical entity. If this phenomenon occurs, then we should see examples of tumors that develop an aggressive histology but are paradoxically prone to extinction. Neuroblastoma, a common childhood cancer, may sometimes fit this pattern. In addition, this model suggests that parenchyma cell diversity can be maintained by a tissue-like integration of cells specialized to provide different services.

Humans↗

PubMed2005

Traveling wave solutions of a reaction diffusion model for competing pioneer and climax species.

Presented is a reaction-diffusion model for the interaction of pioneer and climax species. For certain parameters the system exhibits bistability and traveling wave solutions. Specifically, we show that when the climax species diffuses at a slow rate there are traveling wave solutions which correspond to extinction waves of either the pioneer or climax species. A leading order analysis is used in the one-dimensional spatial case to estimate the wave speed sign that determines which species becomes extinct. Results of these analyses are then compared to numerical simulations of wave front propagation for the model on one and two-dimensional spatial domains. A simple mechanism for harvesting is also introduced.

Animals↗

PubMed2000

The stage-structured predator-prey model and optimal harvesting policy.

In this paper, we establish a mathematical model of two species with stage structure and the relation of predator-prey, to obtain the necessary and sufficient condition for the permanence of two species and the extinction of one species or two species. We also obtain the optimal harvesting policy and the threshold of the harvesting for sustainable development.

Alligators and Crocodiles↗

PubMed1997

Platinum group element enrichments and possible chondritic Ru:Ir across the Frasnian-Famennian boundary, western New York State.

The Frasnian-Famennian boundary is recognized as the culmination of a global mass extinction in the Late Devonian. In western New York State the boundary is a distinct horizon within a pyritic black shale bed of the upper Hanover Shale defined by the first occurrence of Palmatolepis triangularis in the absence of Frasnian conodonts. The boundary is characterized by a minor disconformity marked by a lag concentration of conodonts. Iridium at the boundary is 0.11-0.24 ng/g, two to five times background levels of <0.05 ng/g; other Ir enrichments of 0.38 ng/g and 0.49 ng/g occur within 50 cm of the conodont-constrained boundary. Numerous Ir enrichments in the boundary interval suggest extraterrestrial accretion and platinum group element (PGE) concentration at disconformities, or mobilization and concentration in organic-rich/pyritic-rich laminations from cosmic or terrestrial sources. PGE ratios of Pt/Pd and Ku/Ir at the boundary horizon approximate chondritic ratios and are suggestive of an unaltered extraterrestrial source. These values do not conclusively establish a single extraterrestrial impact as the ultimate cause of the Frasnian-Famennian mass extinction, especially given the presence of similar Ir enrichments elsewhere in the section and the absence at the boundary of microtektites and shocked mineral grains.

Animals↗

PubMed2002

mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Brantacanadensis).

Phylogenetic analysis of 1.35 kb of mtDNA sequence from fossils revealed a previously unknown radiation of Hawaiian geese, of which only one representative remains alive (the endangered Hawaiian goose or nene, Branta sandvicensis). This radiation is nested phylogenetically within a living species, the Canada goose (Branta canadensis) and is related most closely to the large-bodied lineage within that species. The barnacle goose (Branta leucopsis) is also nested within the Canada goose species and is related most closely to the small-bodied lineage of Canada geese. The peripheral isolation of the barnacle goose in the Palearctic apparently allowed the evolution of its distinctive plumage pattern, whereas the two Nearctic lineages of Canada geese share a primitive plumage pattern. The Hawaiian lineage of Canada geese diverged more dramatically, splitting into at least three species that differ in body size, body proportions, and flight ability. One fossil species, limited to the island of Hawaii, was related closely to the nene but was over four times larger, flightless, heavy-bodied and had a much more robust cranium. Application of a rate calibration to levels of DNA divergence suggests that this species evolved on the island of Hawaii in less than 500,000 years. This date is consistent with the potassium/argon-based age of the island of Hawaii of 430,000-500,000 years. The giant Hawaii goose resembles the moa-nalos, a group of massive, extinct, flightless ducks that lived on older Hawaiian Islands and thus is an example of convergent evolution of similar morphologies in island ecosystems.

Animals↗

PubMed2005

Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal.

BACKGROUND: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. RESULTS: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 +/- 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 +/- 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. CONCLUSION: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

Animals↗

PubMed1994

The effects of a pulsed application of chlorpyrifos on macroinvertebrate communities in an outdoor artificial stream system.

The results of an experiment examining the effects of pulsed application of a pesticide, chlorpyrifos, in an outdoor replicated artificial stream system are described. Two levels of chlorpyrifos were used, 0.1 microgram.liter-1 (low dose) and 5.0 micrograms.liter-1 (high dose), and applied for 6 hr. Low-dose streams showed little impact from the treatment and were indistinguishable from control streams. Significant reductions in invertebrate density occurred in the high-dose streams and were mainly due to reductions in density of chironomid larvae. There were no significant reductions in taxon richness associated with the treatments indicating no localized extinctions of species. Diversity measures were insensitive to the changes observed in the streams. Ordination and classification procedures were more illuminating and indicated that the major effect of pesticide application was to interfere with the normal pattern of community change occurring within the system. Recovery following treatment was rapid. The results are discussed with reference to the use of indicator species and biological monitoring strategies intended to identify human-mediated disturbance.

Analysis of Variance↗

PubMed1999

A neural network model with dopamine-like reinforcement signal that learns a spatial delayed response task.

This study investigated how the simulated response of dopamine neurons to reward-related stimuli could be used as reinforcement signal for learning a spatial delayed response task. Spatial delayed response tasks assess the functions of frontal cortex and basal ganglia in short-term memory, movement preparation and expectation of environmental events. In these tasks, a stimulus appears for a short period at a particular location, and after a delay the subject moves to the location indicated. Dopamine neurons are activated by unpredicted rewards and reward-predicting stimuli, are not influenced by fully predicted rewards, and are depressed by omitted rewards. Thus, they appear to report an error in the prediction of reward, which is the crucial reinforcement term in formal learning theories. Theoretical studies on reinforcement learning have shown that signals similar to dopamine responses can be used as effective teaching signals for learning. A neural network model implementing the temporal difference algorithm was trained to perform a simulated spatial delayed response task. The reinforcement signal was modeled according to the basic characteristics of dopamine responses to novel stimuli, primary rewards and reward-predicting stimuli. A Critic component analogous to dopamine neurons computed a temporal error in the prediction of reinforcement and emitted this signal to an Actor component which mediated the behavioral output. The spatial delayed response task was learned via two subtasks introducing spatial choices and temporal delays, in the same manner as monkeys in the laboratory. In all three tasks, the reinforcement signal of the Critic developed in a similar manner to the responses of natural dopamine neurons in comparable learning situations, and the learning curves of the Actor replicated the progress of learning observed in the animals. Several manipulations demonstrated further the efficacy of the particular characteristics of the dopamine-like reinforcement signal. Omission of reward induced a phasic reduction of the reinforcement signal at the time of the reward and led to extinction of learned actions. A reinforcement signal without prediction error resulted in impaired learning because of perseverative errors. Loss of learned behavior was seen with sustained reductions of the reinforcement signal, a situation in general comparable to the loss of dopamine innervation in Parkinsonian patients and experimentally lesioned animals. The striking similarities in teaching signals and learning behavior between the computational and biological results suggest that dopamine-like reward responses may serve as effective teaching signals for learning behavioral tasks that are typical for primate cognitive behavior, such as spatial delayed responding.

Animals↗

PubMed2006

Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities?

Biological invasions dramatically affect the distribution, abundance and reproduction of many native species. Because of these ecological effects, exotic species can also influence the evolution of natives exposed to novel interactions with invaders. Evolutionary changes in natives in response to selection from exotics are usually overlooked, yet common responses include altered anti-predator defenses, changes in the spectrum of resources and habitats used, and other adaptations that allow native populations to persist in invaded areas. Whether a native population is capable of responding evolutionarily to selection from invaders will depend on the demographic impact of the invader, the genetic architecture and genetic variability of the native population and potentially the history of previous invasions. In some cases, natives will fail to evolve or otherwise adapt, and local or global extinction will result. In other cases, adaptive change in natives may diminish impacts of invaders and potentially promote coexistence between invaders and natives. Here, we review the evidence for evolutionary responses of native species to novel community members. We also discuss how the effects of introduced species may differ from those caused by natural range expansions of native species. Notably, introduced species may come from remote biotas with no previous evolutionary history with the native community. In addition, the rate of addition of introduced species into communities is much greater than all but the most extreme cases of historical biotic exchange. Understanding the evolutionary component of exotic/native species interactions is critical to recognizing the long-term impacts of biological invasions, and to understanding the role of evolutionary processes in the assembly and dynamics of natural communities.

Animals↗

PubMed1983

Biological control of insect pests.

Isozyme techniques have proven particularly useful in the past in the field of biological insect control. In this brief review I have tried to give a small selection of the varied approaches that have been used. In the future, isozyme analysis will undoubtedly play a major role. But genetic analyses, as exemplified by the use of isozymes, form but a small part of the knowledge we must have if biological control programs are to be successful. In a pest management program where one is using both chemical and biological methods it is necessary to know a great deal about the biology of the pests, their parasites, predators, and host plants or animals, together with a knowledge of the general ecology of the area where the problem exists. Too often, major control programs have been started with pitifully inadequate basic knowledge of the insect pest concerned, dooming such projects to a series of frantic and generally makeshift attempts to redeem these inadequacies. We are starting to see a much greater emphasis on interrelationships between scientific disciplines, more basic research being conducted, and a resurgence of interaction between those people who are in the applied field and those in the basic sciences. This dialog must be continued. In closing, I want to emphasize again that in pest control we are involved in the management of a coexistence with insects and I think it appropriate to end with the thoughts of W.J. Holland [1949]: when all cities shall have been long dead and crumbled into dust, and all life shall be on the very last verge of extinction on this globe; then on a bit of lichen, growing on the bald rocks beside the eternal snows of Panama, shall be seated a tiny insect, preening its antenna in the glow of the worn-out sun, representing the sole survival of animal life on this our earth--a melancholy 'bug'.

Alleles↗

PubMed1981

Video-enhanced contrast, differential interference contrast (AVEC-DIC) microscopy: a new method capable of analyzing microtubule-related motility in the reticulopodial network of Allogromia laticollaris.

A new method called Allen Video-enhanced Contrast, Differential Interference Contrast (AVEC-DIC) microscopy is shown to be sufficiently sensitive to detect several new features of microtubule-related motility in the reticulopodial network of the foraminifer, Allogromia. The method takes advantage of the variable gain and offset features of a binary video camera to operate the DIC microscope under conditions highly favorable for video imaging, but in which the optical image is virtually invisible to the eye yet retains its full information when viewed by a suitable video camera. The improvements are made possible by setting a dé Senarmont compensator to lambda/9-lambda/4 at maximal working aperture of internally corrected planapochromatic objectives. Under these conditions, the offset feature of the video camera can reject so much stray light from the instrument and specimen that contrast compares favorably with that observed in high-extinction images, and polarizing rectifiers offer scarcely any advantage. Freed from the constraints of the light-limited conditions of DIC microscopy, video images can be recorded 60 times per second, or over 1,000 times the rate of photomicrographs at comparable magnifications under high-extinction conditions. Application of this method to the reticulopodial network of Allogromia has shown that cytoplasmic organelles are translocated only in contact with single microtubules or bundles of microtubules, and that these organelles fail to move when separated from microtubules. Microtubules themselves undergo both axial translatory ("sliding") and lateral "zipping and unzipping" movements that have been suggested to occur during mitosis and other biological processes.

Animals↗

PubMed2001

Predation in the presence of decoys: an inhibitory factor on pathogen control by bacteriophages or bdellovibrios in dense and diverse ecosystems.

Several attempts have been made at the removal of specific pathogens from the intestinal microflora using either bacteriophages or "predatory" bacteria such as Bdellovibrio spp. To date these attempts have had mixed success. A mechanism explaining these findings based on competitive hindrance by non-prey, or decoy species is put forward. It is shown that this hindrance tends to damp out predator-prey oscillations, and therefore reduces the probability of prey extinction. Possible experiments to verify this theory are discussed. The decoy effect may play a role in any system with high densities of bacteria or other particulate matter, such as activated sludge or biofilms.

Bacteria↗

PubMed1987

Persistence, extinction, and critical patch number for island populations.

Sufficient conditions are derived for persistence and extinction of a population inhabiting several islands. Discrete reaction-diffusion population models are analyzed which describe growth and diffusion of a population on a group of islands or a patch environment. A critical patch number is defined as the number of islands below which the population goes extinct on that group of islands. It is shown that population persistence on one island leads to population persistence for the entire archipelago. Both single-species and multi-species models are discussed.

Animals↗

PubMed2001

Stochastic models of a parasitic infection, exhibiting three basic reproduction ratios.

Two closely related stochastic models of parasitic infection are investigated: a non-linear model, where density dependent constraints are included, and a linear model appropriate to the initial behaviour of an epidemic. Host-mortality is included in both models. These models are appropriate to transmission between homogeneously mixing hosts, where the amount of infection which is transferred from one host to another at a single contact depends on the number of parasites in the infecting host. In both models, the basic reproduction ratio R0 can be defined to be the lifetime expected number of offspring of an adult parasite under ideal conditions, but it does not necessarily contain the information needed to separate growth from extinction of infection. In fact we find three regions for a certain parameter where different combinations of parameters determine the behavior of the models. The proofs involve martingale and coupling methods.

Animals↗

PubMed1989

Life on Mars: how it disappeared (if it was ever there).

The cryptoendolithic microbial community in the Ross Desert (McMurdo Dry Valleys) of Antarctica exists at temperatures significantly below the temperature optima of the primary producers. Surviving near the limit of their physiological adaptability, the organisms are under severe environmental stress, so further deterioration in the environment results in cell damage and death. The sequence of events leading to extinction is considered to be a terrestrial analog for disappearance of possible life on early Mars. Progressive stages of cell damage and death in the Ross Desert material are documented with transmission electron microscopy.

Antarctic Regions↗

PubMed2001

Is salivary histatin 5 a metallopeptide?

Histatins are small histidine-rich salivary polypeptides which exhibit antimicrobial activity against Candida albicans. This antimicrobial activity has been ascribed in part to a high content of basic amino acids. However, unlike most other antimicrobial proteins histatins have a high content of histidine, tyrosine and acidic amino acids known to participate in metal ion coordination. This study was conducted to test whether histatin 5 could bind zinc and copper which are metals present in salivary secretions and whole saliva. Physical binding parameters and spectral properties of zinc- and copper-histatin complexes were investigated in order to obtain direct evidence of these interactions. A spectrophotometric competition assay using the metallochromic indicator murexide showed that histatin 5 dissociates metal indicator complexes containing zinc or copper ions. Absorption spectra of histatin 5 at increasing copper chloride concentrations resulted in higher absorbance in the 230-280 nm wavelength range and this spectral change was saturated at a peptide:metal molar ratio of approx. 1:1. A corresponding band was observed in the visible range of the spectrum with a maximum and molar extinction coefficient corresponding to that of copper binding to an ATCUN motif. Quantitative assessment of zinc and copper binding to histatin 5 using isothermal titration calorimetry revealed at least one high affinity site for each metal, with binding constants of 1.2x10(5) and 2.6x10(7) M(-1), respectively. These results indicate that histatin 5 exhibits metallopeptide-like properties. The precise biological significance of this has not yet been established but histatins may contribute significantly to salivary metal binding capacity.

Amino Acid Sequence↗

PubMed1997

A theoretical integration of Cambrian explosion and post-Permian quiescence.

Trophic dynamics is internally causative. Each trophic level is causative in initiating changes in trophic flow either as a supplier towards the upper level or as a consumer towards the lower. Resource presentation followed by its subsequent exploitation makes suppliers causative, while resource exploitation followed by its subsequent presentation makes consumers causative. Trophic dynamics of supplier domination gradually alternates with that of consumer domination while being punctuated by occasional mass extinctions due to depletion of the resources towards the lowest trophic level. The Cambrian explosion could be associated with trophic dynamics of supplier domination, whereas the post-Permian quiescence with that of consumer influencing supplier domination.

Animals↗

PubMed1997

Computational sequence analysis of the tissue inhibitor of metalloproteinase family.

The tissue inhibitor of metalloproteinase (TIMP) family regulates extracellular matrix turnover and tissue remodeling by forming tight-binding inhibitory complexes with matrix metalloproteinases (MMPs). MMPs and TIMPs have been implicated in many normal and pathological processes, such as morphogenesis, development, angiogenesis, and cancer metastasis. This minireview provides information that would aid in classification of the TIMP family and in understanding the similarities and differences among TIMP members according to the physical data, primary structure, and homology values. Calculations of molecular weight, isoelectric point values, and molar extinction coefficients are reported. This study also compares sequence similarities and differences among the TIMP members through calculations of homology within their individual loop regions and the mature region of the molecule. Lastly, this report examines structure-function relationships of TIMPs. Thorough knowledge of TIMP primary and tertiary structure would facilitate the uncovering of the molecular mechanisms underlying metalloproteinase, inhibitory activities and biological functions of TIMPs.

Algorithms↗