Modeling, Simulating, and Parameter Fitting of Biochemical Kinetic Experiments

In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze, requiring numerical methods to approximate the solutions. Compounding this difficulty are the unknown parameters in the DE system, which must be given specific numerical values in order for simulations to be run. Estrogen receptor protein dimerization is used as an example to demonstrate model construction, reduction, simulation, and parameter estimation. Mathematical, computational, and statistical methods are applied to empirical data to deduce kinetic parameter estimates and guide decisions regarding future experiments and modeling. The process demonstrated serves as a pedagogical example of quantitative methods being used to extract parameter values from biochemical data models.Comment: 23 pages, 9 figures, to be published in SIAM Revie

Inversion of initial dominance relationships following the interchange of roles of resident and intruder within pairs of male swordtail fish (Xiphophorus helleri)

This experiment consisted of 75 different pairs composed of two male adults Xiphophorus helleri meeting each other twice. On the first occasion, one of the fish was familiarized with the meeting place for 3h (resident) while its opponent was familiarized with another aquarium (intruder). Upon dominance of one individual over the other, the pair members were separated and returned to their respective home groups for 168 hours (7 days). After this period of separation, the same pair members were reunited and met while roles had been reversed: the initial resident became the intruder, and the initial intruder was given prior-residency. Individuals in the initial resident role defeated the initial intruder in a significant majority of cases (76%). On their second meeting, the newly established dominance relationship was noted in favour of the new resident in a significant majority of cases (82%), and in a reversed direction as compared to the initially established dominance order. This shows that prior-residence is a powerful determinant of dyadic dominance outcome in Xiphophorus males when fish show minimal size differences

Conflict outcome in male green swordtail fish dyads (Xiphophorus helleri): Interaction of body size, prior dominance/subordination experience and prior residency

The relative contribution of asymmetries in prior experience, size, and prior residency to the determination of dyadic dominance between unacquainted individuals was examined using pairs of green swordtail fish, Xiphophorus helleri. Four types of encounters were staged between an intruder and a smaller resident: (1) both had experienced prior victory; (2) both had experienced prior defeat; (3) the intruder had experienced prior victory and the resident prior defeat; and (4) the intruder had experienced prior defeat and the resident prior victory. In a fifth condition in which two intruders met, one was a prior subordinate and the other a prior dominant smaller in size than its opponent. In all these encounters, the superiority in lateral surface of one fish varied between 0 to 30% over that of its opponent. Results showed that (1) when size differences between contestants were within the range of 0-10% and there was an asymmetry in prior social experience, conflicts were essentially resolved according to prior experience with prior winners systematically defeating prior losers; (2) prior residency of 3 hours was an advantage only when both opponents had experienced prior defeat before meeting and when size asymmetries were small (e.g. <20%). It was not an advantage between prior winners or between a prior winner and a prior loser; (3) when large size asymmetries existed (e.g. 20-30%), size uniquely determined dominance outcome and nullified other advantages or disadvantages due to prior social experience and prior residency; and (4) at intermediate levels of size asymmetries (e.g. 10-20%), size partially cancelled any advantage due to a prior victory, and gradually beacme the most important factor in accounting for victories

Outcome of dyadic conflict in male green swordtail fish, Xiphophorus helleri: effects of body size and prior dominance

The relative contribution of prior experience and of size asymmetries to the determination of dyadic dominance between unfamiliar individuals was examined using pairs of green swordtail fish, Xiphophorus helleri. Three experiments were conducted to assess the extent to which superiority in size could override potential handicaps resulting from prior experience. These results indicated that prior experience accounted for dyadic dominance when the size advantage of a previously subordinate over a previously dominant opponent was less than 25 mm2. However, as the lateral surface of the subordinate fish increased, neither previous experience nor size differences clearly accounted for the outcome of dyadic conflict. Even when the size advantage of subordinate opponents was in the 126-150 mm2 range, size differences did not adequately explain the outcome. In conflicts between large previously subordinate and smaller dominant fish, there was evidence for an inverse linear relation between the effects of size and the likelihood of establishing dyadic dominance. In general, males with prior experience as subordinates had to be at least 40% larger than a previously dominant fish to win a significant proportion of conflicts. These results indicate that prior agonistic experience and body size effects can be additive when at the advantage of one opponent. These factors can also cancel each other out when in opposition, at least when size differences are not extreme. The results also confirm the main effect of both factors as well as their interaction in the determination of conflict outcomes for X. helleri

Climate Change Leads to a Reduction in Symbiotic Derived Cnidarian Biodiversity on Coral Reefs

Symbiotic relationships enable partners to thrive and survive in habitats where they would either not be as successful, or potentially not exist, without the symbiosis. The coral reef ecosystem, and its immense biodiversity, relies on the symbioses between cnidarians (e.g., scleractinian corals, octocorals, sea anemones, jellyfish) and multiple organisms including dinoflagellate algae (family Symbiodiniaceae), bivalves, crabs, shrimps, and fishes. In this review, we discuss the ramifications of whether coral reef cnidarian symbioses are obligatory, whereby at least one of the partners must be in the symbiosis in order to survive or are facultative. Furthermore, we cover the consequences of cnidarian symbioses exhibiting partner flexibility or fidelity. Fidelity, where a symbiotic partner can only engage in symbiosis with a subset of partners, may be absolute or context dependent. Current literature demonstrates that many cnidarian symbioses are highly obligative and appear to exhibit absolute fidelity. Consequently, for many coral reef cnidarian symbioses, surviving changing environmental conditions will depend on the robustness and potential plasticity of the existing host-symbiont(s) combination. If environmental conditions detrimentally affect even one component of this symbiotic consortium, it may lead to a cascade effect and the collapse of the entire symbiosis. Symbiosis is at the heart of the coral reef ecosystem, its existence, and its high biodiversity. Climate change may cause the demise of some of the cnidarian symbioses, leading to subsequent reduction in biodiversity on coral reefs

Comparative Study of \u3ci\u3eMecinus Janthiniformis\u3c/i\u3e (Coleoptera: Curculionidae) Attack and Simulated Mowing for Control of \u3ci\u3eLinaria Dalmatica\u3c/i\u3e Spp. \u3ci\u3eDalmatica\u3c/i\u3e (Plantaginaceae)

Dalmatian toadflax, Linaria dalmatica spp. dalmatica (L.) Mill. (Plantaginaceae) has invaded over one million hectares in the western United States and Canada, in habitats similar to its native range. Two field studies were conducted to examine the impact of simulated mowing or insect herbivory on L. dalmatica growth and reproduction. Simulated mowing over the duration of the study decreased L. dalmatica total biomass per square meter, significantly reduced the total number of fruits and flowers per square meter, and resulted in significantly shorter flowering stems in the simulated mowing plots than in their controls. Plants in plots attacked by Mecinus janthiniformis Toševski and Caldara (Coleoptera: Curculionidae) had significantly less biomass per square meter, significantly fewer total numbers of fruits and flowers per square meter, and significantly fewer reproductive structures per stem than plants in paired control plots over the duration of the study. Specifically, both management tactics resulted in a negative impact on this invasive plant. With repeated tissue removal or damage, a reduction in numbers of fruits and flowers per stem on both the stems subjected to simulated mowing and Mecinus-attacked stems relative to their controls suggests that long term stress effects on the plants may be similar. The results of these studies suggest that mowing may warrant further evaluation as a possible method of control in areas where M. janthiniformis release is not effective