Implementing behaviour in individual-based models using neural networks and genetic algorithms

Even though individual-based models (IBMs) have become very popular in ecology during the last decade, there have been few attempts to implement behavioural aspects in IBMs. This is partly due to lack of appropriate techniques. Behavioural and life history aspects can be implemented in IBMs through adaptive models based on genetic algorithms and neural networks (individual-based-neural network-genetic algorithm, ING). To investigate the precision of the adaptation process, we present three cases where solutions can be found by optimisation. These cases include a state-dependent patch selection problem, a simple game between predators and prey, and a more complex vertical migration scenario for a planktivorous fish. In all cases, the optimal solution is calculated and compared with the solution achieved using ING. The results show that the ING method finds optimal or close to optimal solutions for the problems presented. In addition it has a wider range of potential application areas than conventional techniques in behavioural modelling. Especially the method is well suited for complex problems where other methods fail to provide answers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Uracil in DNA--general mutagen, but normal intermediate in acquired immunity

Deamination of cytosine in DNA results in mutagenic U:G mispairs, whereas incorporation of dUMP leads to U:A pairs that may be genotoxic directly or indirectly. In both cases, uracil is mainly removed by a uracil-DNA glycosylase (UDG) that initiates the base excision repair pathway. The major UDGs are mitochondrial UNG1 and nuclear UNG2 encoded by the UNG-gene, and nuclear SMUG1. TDG and MBD4 remove uracil from special sequence contexts, but their roles remain poorly understood. UNG2 is cell cycle regulated and has a major role in post-replicative removal of incorporated uracils. UNG2 and SMUG1 are both important for prevention of mutations caused by cytosine deamination, and their functions are non-redundant. In addition, SMUG1 has a major role in removal of hydroxymethyl uracil from oxidized thymines. Furthermore, UNG-proteins and SMUG1 may have important functions in removal of oxidized cytosines, e.g. isodialuric acid, alloxan and 5-hydroxyuracil after exposure to ionizing radiation. UNG2 is also essential in the acquired immune response, including somatic hypermutation (SHM) required for antibody affinity maturation and class switch recombination (CSR) mediating new effector functions, e.g. from IgM to IgG. Upon antigen exposure B-lymphocytes express activation induced cytosine deaminase that generates U:G mispairs at the Ig locus. These result in GC to AT transition mutations upon DNA replication and apparently other mutations as well. Some of these may result from the generation of abasic sites and translesion bypass synthesis across such sites. SMUG1 can not complement UNG2 deficiency, probably because it works very inefficiently on single-stranded DNA and is down-regulated in B cells. In humans, UNG-deficiency results in the hyper IgM syndrome characterized by recurrent infections, lymphoid hyperplasia, extremely low IgG, IgA and IgE and elevated IgM. Ung(-/-) mice have a similar phenotype, but in addition display dysregulated cytokine production and develop B cell lymphomas late in life.     

Predicting the potential demographic impact of predators on their prey: a comparative analysis of two carnivore-ungulate systems in Scandinavia

1. Understanding the role of predation in shaping the dynamics of animal communities is a fundamental issue in ecological research. Nevertheless, the complex nature of predator-prey interactions often prevents researchers from modelling them explicitly. 2. By using periodic Leslie-Usher matrices and a simulation approach together with parameters obtained from long-term field projects, we reconstructed the underlying mechanisms of predator-prey demographic interactions and compared the dynamics of the roe deer-red fox-Eurasian lynx-human harvest system with those of the moose-brown bear-gray wolf-human harvest system in the boreal forest ecosystem of the southern Scandinavian Peninsula. 3. The functional relationship of both roe deer and moose λ to changes in predation rates from the four predators was remarkably different. Lynx had the strongest impact among the four predators, whereas predation rates by wolves, red foxes, or brown bears generated minor variations in prey population λ. Elasticity values of lynx, wolf, fox and bear predation rates were -0·157, -0·056, -0·031 and -0·006, respectively, but varied with both predator and prey densities. 4. Differences in predation impact were only partially related to differences in kill or predation rates, but were rather a result of different distribution of predation events among prey age classes. Therefore, the age composition of killed individuals emerged as the main underlying factor determining the overall per capita impact of predation. 5. Our results confirm the complex nature of predator-prey interactions in large terrestrial mammals, by showing that different carnivores preying on the same prey species can exert a dramatically different demographic impact, even in the same ecological context, as a direct consequence of their predation patterns. Similar applications of this analytical framework in other geographical and ecological contexts are needed, but a more general evaluation of the subject is also required, aimed to assess, on a broader systematic and ecological range, what specific traits of a carnivore are most related to its potential impact on prey species.     

Alveolar hypoxia induces left ventricular diastolic dysfunction and reduces phosphorylation of phospholamban in mice

Chronic obstructive pulmonary disease (COPD) may lead to pulmonary hypertension (PH) and reduced function of the right ventricle (RV). However, COPD patients may also develop left ventricular (LV) diastolic dysfunction. We hypothesized that alveolar hypoxia induces LV diastolic dysfunction and changes in proteins governing Ca(2+) removal from cytosol during diastole. Mice exposed to 10% oxygen for 1, 2, or 4 wk were compared with controls. Cardiac hemodynamics were assessed with Doppler echocardiography and a microtransducer catheter under general anesthesia. The pulmonary artery blood flow acceleration time was shorter and RV pressure was higher after 4 wk of hypoxia compared with controls (both P < 0.05). In the RV and LV, 4 wk of hypoxia induced a prolongation of the time constant of isovolumic pressure decay (51% RV, 43% LV) and a reduction in the maximum rate of decline in pressure compared with control (42% RV, 42% LV, all P < 0.05), indicating impaired relaxation and diastolic dysfunction. Alveolar hypoxia induced a 38%, 47%, and 27% reduction in Ser16-phosphorylated phospholamban (PLB) in the RV after 1, 2, and 4 wk of hypoxia, respectively, and at the same time points, Ser16-phosphorylated PLB in the LV was downregulated by 32%, 34%, and 25% (all P < 0.05). The amounts of PLB and sarco(endo)plasmic reticulum Ca(2+) ATPase (SERCA2a) were not changed. In conclusion, chronic alveolar hypoxia induces hypophosphorylation of PLB at Ser16, which might be a mechanism for impaired relaxation and diastolic dysfunction in both the RV and LV.     

Perfused hearts from Type 2 diabetic (db/db) mice show metabolic responsiveness to insulin

Diabetic (db/db) mice provide an animal model of Type 2 diabetes characterized by marked in vivo insulin resistance. The effect of insulin on myocardial metabolism has not been fully elucidated in this diabetic model. In the present study we tested the hypothesis that the metabolic response to insulin in db/db hearts will be diminished due to cardiac insulin resistance. Insulin-induced changes in glucose oxidation (GLUox) and fatty acid (FA) oxidation (FAox) were measured in isolated hearts from control and diabetic mice, perfused with both low as well as high concentration of glucose and FA: 10 mM glucose/0.5 mM palmitate and 28 mM glucose/1.1 mM palmitate. Both in the absence and presence of insulin, diabetic hearts showed decreased rates of GLUox and elevated rates of FAox. However, the insulin-induced increment in GLUox, as well as the insulin-induced decrement in FAox, was similar or even more pronounced in diabetic that in control hearts. During elevated FA and glucose supply, however, the effect of insulin was blunted in db/db hearts with respect to both FAox and GLUox. Finally, insulin-stimulated deoxyglucose uptake was markedly reduced in isolated cardiomyocytes from db/db mice, whereas glucose uptake in isolated perfused db/db hearts was clearly responsive to insulin. These results show that, despite reduced insulin-stimulated glucose uptake in isolated cardiomyocytes, isolated perfused db/db hearts are responsive to metabolic actions of insulin. These results should advocate the use of insulin therapy (glucose-insulin-potassium) in diabetic patients undergoing cardiac surgery or during reperfusion after an ischemic insult.     

Effects of clutch sizes and incubation stage on nest desertion in the female Common Eider Somateria mollissima nesting in the high Arctic

In bird species, one of the trade-offs between reproduction and survival appears in the parental decision to desert the nest. Nest desertion is modulated by several factors including clutch size. However, the incubation stage at which predation occurs is also an important factor. In this study, we examined whether nest desertion was linked to initial clutch size, partial clutch predation (final clutch size) and the incubation stage at which it happened in a capital breeder: the female common eider (Somateria mollissima) nesting in the high Arctic. The study was performed in Kongsfjorden in 2002 on the western coast of the Svalbard Archipelago (78°55′N, 20°07′E). We observed that nest desertion was higher when the initial clutch size was small. Also, females deserted their nests more during the first third of incubation than later. Thus, as incubation proceeded, nest desertion was less likely to occur even after egg reduction. Our results pointed out that this parental decision in female eiders seemed to depend on initial clutch size and on the date into incubation of clutch reduction. Sophie Bourgeon and Francois Criscuolo contributed equally to the work     

Sperm velocity and its relation to social status in Arctic charr (Salvelinus alpinus)

Sperm velocity has been shown to be a major determinant of fertilization success of external fertilizers. Yet, sperm velocity varies both within and between ejaculates and only a small number of fast sperm cells within an ejaculate are likely to have the potential of fertilizing the eggs. Having such fast cells should be of special importance during sperm competition, particularly for subordinate males that may release their sperm later or further away from eggs, than dominants. We examined ejaculates of dominant and subordinate male Arctic charr (Salvelinus alpinus), a species with sperm competition. Yet, rather than examining just average sperm velocity values, the aim was to examine whether the fastest fraction of sperm cell from dominant and subordinate males differed in velocity. While there was no difference in the average sperm velocity between dominant and subordinate males, analysis of the fastest swimming sperm cells show that subordinate males have significantly higher initial sperm velocity than dominant males within the 10, 5 and 1% fastest sperm cells. That is, the difference in sperm velocity between dominant and subordinate charr is most predominant among the fastest sperm cells. In sum, this study emphasizes the importance of studying the fastest sperm cells in the ejaculates, as status-dependent differences in sperm velocity may not be detected using average values.