A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks

Background  

The fundamental role that intrinsic stochasticity plays in cellular functions has been shown via numerous computational and experimental studies. In the face of such evidence, it is important that intracellular networks are simulated with stochastic algorithms that can capture molecular fluctuations. However, separation of time scales and disparity in species population, two common features of intracellular networks, make stochastic simulation of such networks computationally prohibitive. While recent work has addressed each of these challenges separately, a generic algorithm that can simultaneously tackle disparity in time scales and population scales in stochastic systems is currently lacking. In this paper, we propose the hybrid, multiscale Monte Carlo (HyMSMC) method that fills in this void.     

Food preference,food quality and diets of three herbivorous gastropods (Trochidae: Tegula) in a temperate kelp forest habitat

Summary The relationship between food preference and food quality (i.e. a food's contribution to growth and reproductive development) was examined in the laboratory for 3 species of herbivorous kelp forest gastropods (Tegula). The preference hierarchies of the 3 Tegula for 6 common algal species are the same: giant kelp (Macrocystis) is the most preferred food and brown algae are consumed at higher rates than red algae. Despite their strong preference for Macrocystis, the 3 species had significantly greater growth and/or reproductive development on a mixed-algae diet than on either brown or red algae alone. Laboratory preferences of the snails did not correspond closely with caloric content, estimated availability or quality of the algal species used in this study. However, the 3 Tegula are subject to strong benthic predation and Macrocystis provides an important spatial refuge in nature. The potential role of non-nutritional factors such as predator avoidance on the formation of food preferences is discussed.     

Ontogenetic changes in food intake and digestion rate of the herbivorous marine iguana (Amblyrhynchus cristatus,Bell)

Young reptiles have higher relative energy demands than adults, but the proposed ontogenetic changes in diet to fulfil these demands were not found in the algae-eating Galápagos marine iguanas on Santa Fé. Feeding and digestion rates were investigated to analyse how young achieve higher energy intake. Daily food intake of free ranging marine iguana hatchlings (6–11 months old) was about one third that of adults, but relative intake (g dry mass · g^–1 wet mass · day^–1) was four times higher in the hatchlings. During feeding experiments, relative daily food intake of hatchling marine iguanas was approximately three times higher than that of adults (0.042 vs 0.013 g dry mass · g^–0.8 wet mass · day^–1), and mean gut passage time was two times shorter (5 vs 10 days). The hatchlings also maintained high body temperatures (36.7° C) even under relatively cool day-time air temperatures of 32° C. Apparent digestibility of algal food measured both during feeding trials and by Mn²⁺ AAS (atomic absorption spectrometry) for free-ranging iguanas was 70%, independent of body size and temperature. The red algae prevailing in the diet were high in protein (30% dry mass) and energy (12.1 kJ/g dry mass). Diving iguanas had higher rates of energy intake than intertidal foragers, but daily intake was less. Maintenance of high body temperature enabled hatchlings to achieve high digestion rates and, combined with high relative intake, thus achieve sufficient energy intake for rapid growth despite higher mass specific metabolic rates. Estimates of biomass of marine iguanas and their algal food are given for a section of coastline on Santa Fé.     

Oral food processing in two herbivorous lizards, Iguana iguana (Iguanidae) and Uromastix aegyptius (Agamidae).

The anatomy and function of the feeding apparatus in Iguana iguana and Uromastix aegyptius were studied by dissection, cinematic and cineradiographic techniques. The feeding behavior of these species differs from that of insectivorous lizards in the cropping action involves movement of both the upper jaw around the atlantooccipital joint and the lower jaw around the mandibular joint; and in Uromastix only, streptostylic movement of the quadrate. Often movements of the whole head play a supplementary role in the cropping action. In both species the feeding apparatus has been modified to facilitate cropping. In Iguana the pleurodont dentition is multicusped and laterally compressed. Each tooth forms a shearing blade whose function does not require contact with other teeth. In Uromastix the dentition is acrodont and the cheek teeth are massive and lack cusps. Occlusion is necessary for shearing plant material. The skull system of Uromastix also has a number of modified structures which allow protraction and retraction of the lower jaw to facilitate cropping while maintaining a gape equivalent to that in Iguana. It is suggested that the differences in the feeding apparatus between Iguana and Uromastix are attributable to differeces in the mode of tooth replacement and implantation.     

Digestion time and reemergence in the desert grassland scorpion Paruroctonus utahensis (Williams) (Scorpionida,Vaejovidae)

Summary The desert grassland scorpion Paruroctonus utahensis spends most of its life in its burrow. During the active season, only about 5% of the individuals in a population appear on the surface each night. Individuals do not appear on the surface for several nights following a meal. To determine if physiological digestion time could account for this delay in reemergence after eating, I measured changes in oxygen consumption immediately following a meal. Oxygen consumption exceeded 125 l O₂g^-1h^-1 just after completion of a meal, then dropped to normal levels (53 l O₂g^-1h^-1) within 6 h. I also measured the interval between completion of the meal and subsequent defecation. All individuals defecated by 72 h following ingestion (median 12 h). In field enclosures, scorpions returned to the surface after a mean of 20.3 days (median=16) following a successful predation event. Lack of correspondence between estimates of physiological digestion time and the reappearance interval lead me to reject the idea of a long digestive pause in Paruroctonus utahensis. This conclusion lends support to the hypothesis that scorpions remain in their burrows to minimize exposure to predation.     

Modelling temperature,photoperiod and vernalization responses of Brunonia australis (Goodeniaceae) and Calandrinia sp. (Portulacaceae) to predict flowering time

Background and Aims

Crop models for herbaceous ornamental species typically include functions for temperature and photoperiod responses, but very few incorporate vernalization, which is a requirement of many traditional crops. This study investigated the development of floriculture crop models, which describe temperature responses, plus photoperiod or vernalization requirements, using Australian native ephemerals Brunonia australis and Calandrinia sp.

Methods

A novel approach involved the use of a field crop modelling tool, DEVEL2. This optimization program estimates the parameters of selected functions within the development rate models using an iterative process that minimizes sum of squares residual between estimated and observed days for the phenological event. Parameter profiling and jack-knifing are included in DEVEL2 to remove bias from parameter estimates and introduce rigour into the parameter selection process.

Key Results

Development rate of B. australis from planting to first visible floral bud (VFB) was predicted using a multiplicative approach with a curvilinear function to describe temperature responses and a broken linear function to explain photoperiod responses. A similar model was used to describe the development rate of Calandrinia sp., except the photoperiod function was replaced with an exponential vernalization function, which explained a facultative cold requirement and included a coefficient for determining the vernalization ceiling temperature. Temperature was the main environmental factor influencing development rate for VFB to anthesis of both species and was predicted using a linear model.

Conclusions

The phenology models for B. australis and Calandrinia sp. described development rate from planting to VFB and from VFB to anthesis in response to temperature and photoperiod or vernalization and may assist modelling efforts of other herbaceous ornamental plants. In addition to crop management, the vernalization function could be used to identify plant communities most at risk from predicted increases in temperature due to global warming.     

Adaptation to abundant low quality food improves the ability to compete for limited rich food in Drosophila melanogaster

The rate of food consumption is a major factor affecting success in scramble competition for a limited amount of easy-to-find food. Accordingly, several studies report positive genetic correlations between larval competitive ability and feeding rate in Drosophila; both become enhanced in populations evolving under larval crowding. Here, we report the experimental evolution of enhanced competitive ability in populations of D. melanogaster previously maintained for 84 generations at low density on an extremely poor larval food. In contrast to previous studies, greater competitive ability was not associated with the evolution of higher feeding rate; if anything, the correlation between the two traits across lines tended to be negative. Thus, enhanced competitive ability may be favored by nutritional stress even when competition is not intense, and competitive ability may be decoupled from the rate of food consumption.     

Combined effects of food quantity and quality on Cd, Cr, and Zn assimilation to the green mussel, Perna viridis

We examined the assimilation of Cd, Cr, and Zn by the green mussel Perna viridis under complicated food conditions, including combinations of different compositions and concentrations of food (diatom and sediment), and variable food quantity and quality during particle digestion. At different combinations of food composition and quantity (5 mg l⁻¹ and 20 mg⁻¹, below and above the pseudofeces production), the Cd assimilation was significantly dependent on the food composition. The Cd assimilation efficiency (AE) decreased with increasing proportions of sediments in the diets, but its assimilation was not significantly affected by food concentration. In contrast, the assimilation of Cr and Zn decreased significantly with increasing food concentrations, whereas food composition did not significantly affect their AEs. Variations in metal gut passage time accounted partially for the difference in AEs among different combinations of food composition and quantity. By changing the type of particles during metal digestion, their AEs were maintained comparably at a low particle load (1 mg l⁻¹), suggesting that variation of food quality during digestion did not affect metal assimilation. At a higher particle load (5 mg l⁻¹), variation of food type during digestion affected the AEs of Cr and Zn. An increase in food concentrations from 1 to 15 mg l⁻¹ during digestion resulted in a significant decrease in the AEs of Cr and Zn bound with either sediments or diatoms. Conversely, decreasing the food concentrations from 15 to 1 mg l⁻¹ did not affect the AEs of metals, except for Zn bound with diatoms. Overall, our results highlighted the metal-specificity in their assimilation as influenced by complicated food environments, probably caused by different metal geochemical and biological behavior in the mussels. Feeding selectivity may have a greater control on the influx rate into the mussels than metal assimilation.     

Hybrid origins and F1 dominance in the free-floating, sterile bladderwort, Utricularia australis f. australis (Lentibulariaceae)

Abandonment of sexual reproduction is a well-known characteristic in aquatic plants, while the causes, levels, and consequences of sterility are often unknown. Utricularia australis f. australis (Lentibulariaceae) is a free-floating, sterile bladderwort distributed widely in temperate and tropical regions. Experimental crosses in cultivated conditions, AFLP analysis, and cpDNA haplotypes of natural populations clearly demonstrated that U. australis f. australis originates from the asymmetric hybridization between two parental taxa: U. australis f. tenuicaulis (mostly as female) and U. macrorhiza (mostly as male). No post-F(1) hybrids were detected using the additive patterns of AFLP bands combined with the observation of extensive sterility in U. australis f. australis. Recurrent hybridizations and subsequent perpetuation by asexual reproduction were demonstrated by the unique, but monomorphic, AFLP genotypes observed in each U. australis f. australis population. Hybrids and parental species did not coexist, implying the superiority of the hybrid U. australis f. australis in certain environmental conditions. It remains unclear whether populations of U. australis f. australis are maintained by colonizing propagules or as relicts of past hybridization events.     

Influence of diet on growth,food retention time,and gill ventilation rate of nymphs of Cloeon sp. (Ephemeroptera: Baetidae)

Early instar nymphs of the mayfly, Cloeon sp. were kept on an algal or a detrital diet at 20 ± 1 °C in the laboratory. A control group was not given any food. Nymphs kept on algae showed significantly (P = 0.001) higher growth both in terms of length and biomass than for those kept on detritus. None of the nymphs given algae or detritus died during the experiment, and 40 per cent of those fed algae and 20 per cent fed detritus reached maturity by the termination of the experiment. Food retention time as well as gill ventilation rate of nymphs feeding on algae were significantly (P = 0.001) higher than those feeding on detritus. It is probable that these two factors largely enabled the nymphs to survive as well as to grow and reach maturity, though relatively slowly, solely on a detrital diet. However, algae was clearly shown to be a superior food resource for Cloeon sp. nymphs.     

Linking small desert mammal distribution to habitat structure in a protected and grazed landscape of the Monte, Argentina

Interpretation of landscape patterns from the perspective of different species allows knowing the way in which they perceive landscape, and how their perception varies with scale. We examined distribution of four small mammal species at different scales over a landscape including protected and grazed areas, and associated species distribution with landscape structure. The study was conducted in the central Monte Desert (Reserve of Ñacuñán). Trap grids were set in both areas at two scales, varying their grain and extent. To determine whether spatial patterns are random, clumped or regular, we used a point pattern analysis. Logistic regressions were performed to relate the presence-absence of small mammals to environmental variables. Intensity of the point pattern was not constant, either in the Reserve or the grazed area. Small mammal abundance exhibited a heterogeneous distribution, and the existence of a first-order effect was detected for all species. No second-order effects were detected, the point pattern was random for all species in both areas. Both areas were differently perceived by rodent species. Habitat structure in both conditions and its variations with scale appear to be important factors affecting distribution patterns.     

Modelling the response of phytoplankton in a shallow lake (Loch Leven,UK) to changes in lake retention time and water temperature

The phytoplankton community of Loch Leven in 2005 was modelled and subjected to a combination of different flushing rates and water temperatures in order to assess the lake’s sensitivity to these two climatic drivers. Whilst the simulated annual mean total chlorophyll a proved relatively insensitive to these changes, at the species level marked changes were recorded. Some species responded positively to increased temperature (e.g. Aulacoseira), some negatively (e.g. Asterionella), whilst others were negatively affected by increased flow (e.g. Aphanocapsa) and others enhanced (e.g. Stephanodiscus). However, this relationship with flow was season dependent with, for example, a simulated increase in summer inflows actually benefiting some species through increased nutrient supply, whereas an equivalent increase in flow in wetter seasons would have negatively affected those species (i.e. through flushing loss). Overall, the simulations showed that the range of species types simulated in the community was sufficient for one species to always benefit from the changing niches created by the multiple climatic drivers applied in this study. The level of exploitation by such a species was only constrained by the nutrient carrying capacity of the system, which led to the overall dampened response in the total chlorophyll a measure, both at the annual and season scale. Thus, whilst overall biomass showed relatively little reaction to the two climatic drivers tested, the phytoplankton community composition responded markedly.     

The effects of hydraulic retention time and sludge retention time on the fate of di-(2-ethylhexyl) phthalate in a laboratory-scale anaerobic-anoxic-aerobic activated sludge system

A laboratory-scale anaerobic-anoxic-aerobic (AAA) activated sludge wastewater treatment system was employed to investigate the effects of hydraulic retention time (HRT) and sludge retention time (SRT) on the removal and fate of di-(2-ethylhexyl) phthalate (DEHP). In the range from 5 to 14h, HRT had no significant effect on DEHP removal. However, longer HRT increased DEHP accumulation in the system and DEHP retention in the waste sludge. When SRT was increased from 15 to 25d, DEHP removal efficiency stayed above 96%. Compared to the removal of only 88% at SRT of 10d, longer SRT enhanced DEHP degradation efficiency. The optimal HRT and SRT for both nutrients (nitrogen and phosphorus) and DEHP removal were 8h and 15d. At these retention times, about 71% of DEHP was degraded by the activated sludge process, 26% was accumulated in the system, 2% was released in the effluent, and 1% remained in the waste sludge. The anaerobic, anoxic and aerobic reactors were responsible for 15%, 19% and 62% of the overall DEHP removal, respectively.     

The influence of the quantity of food on fecundity in the desert grassland scorpion (Paruroctonus utahensis) (Scorpionida,Vaejovidae): An experimental test

Summary Females of the desert grassland scorpion Paruroctonus utahensis were maintained in field enclosures and fed differing amounts of food. The number of young scorpions per female varied from 0 to 32. The mean weight of second-instar young varied significantly among broods. The number of young, the size of the young, and total brood weight were not related to adult female size. There were no significant relationships between any of the brood characteristics and the amount of food eaten by the mother during the 11 month gestation. This suggests that foraging success is not an important proximate factor influencing fecundity in Paruroctonus utahensis.     

Growth dynamics of a ctenophore (Mnemiopsis) in relation to variable food supply. I. Carbon biomass, feeding, egg production, growth and assimilation efficiency

This paper contains new experimental data on the growth dynamicsof a lobate coastal ctenophore, Mnenmiopsis mccradyi, whichadd significantly to our understanding of the nutritional ecologyof ctenophores and their role as opportunistic predators. Theseexperimental observations were necessary to refine the dynamiccarbon budget presented as a simulation model in another report.The ratio of carbon biomass to dry weight may vary several-folddepending on the nutritional state and size from >12% inwell-fed larvae to <1% in starved adults. Feeding effort(clearance rate) is higher for previously starved animals, fallingsharply within a few hours after re-exposure to food. Directvisual observations of feeding activity of animals confirmedthis. Assimilation efficiency can be high (72%) in these animalsbut if they continue to feed at high food concentrations, incomingfood displaces material which is only partially digested andassimilation efficiency decreases substantially. Except at verylow food concentrations, growth efficiency ranges between 20and 45%. Mnemiopsis, begins to produce eggs at a size much lessthan its maximum. Egg production is very sensitive to food supply,and somatic growth is favored over egg production at low fooddensities. Even though several thousand eggs may be producedover a few days, they represent <2% day^–1 of the carbonbiomass of the ctenophore and several-fold less than respiratorycarbon.     

Artificial miniaturization causes eggs laid by crowd-reared (gregarious) desert locusts to produce green (solitarious) offspring in the desert locust, Schistocerca gregaria

The mechanism underlying the phase-dependent polyphenism in hatchling body coloration was studied by testing for a possible causal relationship with egg size in the desert locust, Schistocerca gregaria. Crowd-reared (gregarious) females typically produce large, black offspring, whereas females reared in isolation (solitarious) deposit small, green offspring. We first tested for possible genetic differences in the role of egg foam by washing or separating eggs from two strains of locust. No solitarizing effect was found in either of the strains tested, supporting a previous finding, using another laboratory strain, to show that the hatchling body coloration and size are pre-determined in the ovary of the mother and no egg foam factor is involved in the control of the hatchling body coloration. Topical application of fenoxycarb, a juvenile hormone analog (JHA), and implantation of extra corpora allata (CA), taken from Locusta migratoria, caused gregarious female adults of S. gregaria to produce small eggs. Some eggs laid by CA-implanted females produced green hatchlings. All large eggs chosen among those deposited by gregarious females produced black hatchlings. When eggs were either kept on dry filter paper at nearly saturated relative humidity during embryogenesis or pricked with a needle so that some egg yolk was squeezed out, some produced small, green hatchlings. These results suggested that the amount of egg yolk or the availability of yolk material may determine the body coloration of hatchlings.     

Factors affecting follicular population, oocyte yield and quality in camels (Camelus dromedarius) ovary with special reference to maturation time in vitro

Three experiments were conducted to study a series of factors affecting in vitro reproductive parameters in camels. In Experiment 1, the effect of season and presence of a corpus luteum (CL) on ovarian follicular populations, oocyte yield and quality was studied using a total of 252 and 208 ovaries collected during the breeding and non-breeding season, respectively. Small, medium, large and the total number of ovarian follicles, oocyte yield and quality were measured. In Experiment 2, the effect of methods of oocyte retrieval and needle gauge on oocyte yield and quality was evaluated with oocytes recovered using slicing and aspiration with 18-, 19- or 20-gauge needle. Oocytes were evaluated microscopically and classified into three categories. The objective of Experiment 3 was to identify the optimum time for oocyte maturation in the dromedary camel. Oocytes were cultured in CR1aa medium at 38.5 degrees C under 5% CO(2) for 24, 32, 36, 48 and 72h. Maturation was calculated as the percentage of cumulus expansion and oocytes reaching metaphase II (MII). The number of small, medium, large and the total number of ovarian follicles were higher (P<0.01) during the breeding than non-breeding season. The recovery of total number of oocytes and Category I oocytes were also greater (P<0.01) during the breeding season. Ovaries without a CL possessed significantly (P<0.01) more ovarian follicles and more (P<0.05) small and large follicles. The total number of oocytes and Category I oocytes were also greater (P<0.01) in ovaries without CL. Slicing of camel ovaries increased (P<0.01) the yield of oocytes as compared to aspiration. The aspiration of follicles using a 20-gauge needle had greater yields of the total number of oocytes and Category I oocytes than when using 19- (P<0.05) and 18-gauge needle (P<0.01). The culture of camel oocytes for 36h produced higher (P<0.01) percentages of cumulus expansion and oocytes at MII. Increasing culture times up to 48 or 72h increased (P<0.01) the percentage of degenerated oocytes.In conclusion, the growth and development of ovarian follicles in the camel as well as yields of Category I oocyte were greater during the breeding season. Slicing or aspirations using a 20-gauge needle yielded greater numbers of total and Category I oocytes. Finally, maturation of oocytes in CR1aa medium for 36h produced higher percentages of cumulus expansion and oocytes at MII stage.     

Cathemerality in the Mayotte brown lemur (Eulemur fulvus): seasonality and food quality

In past decades, cathemerality--as defined by Tattersall [1987]--has been documented in two primate families: Cebidae and Lemuridae. In the Lemuridae, in particular the genus Eulemur, cathemeral activity seems to be a regular behavioural trait. Nevertheless, ultimate and proximate determinants responsible for this behaviour remain unclear. In this study, in a dry and deciduous forest on Mayotte (Comoro Archipelago), activities of 4 female brown lemurs (Eulemur fulvus fulvus) were recorded by focal animal sampling during the daylight period and by scan sampling on their respective groups during the night. Horizontal distances travelled by females and groups were measured using GPS. During the daylight period, food intakes were estimated in grams by extrapolation of counting of mouthfuls after weighing a large sample of plant parts eaten. Crude protein, crude lipid, soluble sugar and crude fibre were analyzed for each seasonal reconstituted diet. Records of temperature and rainfall were supplied by a local meteorological station. Observations confirmed cathemerality in the Mayotte brown lemur as reported by Tattersall in 1977. During the dry season, the animals increased their nocturnal activity--substantially increasing the time devoted to feeding and moving overall, but especially at night--and were less active during the daylight period. The quality of their diet in the dry season was poorer than that in the wet season, with soluble sugar content and protein content decreasing and fibre content increasing slightly. As a result, Mayotte brown lemurs may need to extend their foraging activity over the 24-hour cycle to balance nutritional requirements.