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.     

Livestock Settlement Dynamics in Drylands: Model application in the Monte desert (Mendoza,Argentina)

Human settlements in arid environments are becoming widespread due to population growth, and without planning, they may alter vegetation and ecosystem processes, compromising sustainability. We hypothesize that in an arid region of the central Monte desert (Mendoza, Argentina), surface and groundwater availability are the primary factors controlling livestock settlements establishment and success as productive units, which affect patterns of degradation in the landscape. To evaluate this hypothesis we simulated settlement dynamics using a Monte Carlo based model of Settlement Dynamics in Drylands (SeDD), which calculates probabilities on a gridded region based on six environmental factors: groundwater depth, vegetation type, proximity to rivers, paved road, old river beds, and existing settlements. A parameter sweep, including millions of simulations, was run to identify the most relevant factors controlling settlements. Results indicate that distances to rivers and the presence of old river beds are critical to explain the current distribution of settlements, while vegetation, paved roads, and water table depth were not as relevant to explain settlement distribution. Far from surface water sources, most settlements were established at random, suggesting that pressures to settle in unfavorable places control settlement dynamics in those isolated areas. The simulated vegetation, which considers degradation around livestock settlements, generally matched the spatial distribution of remotely sensed vegetation classes, although with a higher cover of extreme vegetation classes. The model could be a useful tool to evaluate effects of land use changes, such as water provision or changes on river flows, on settlement distribution and vegetation degradation in arid environments.     

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.     

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.     

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.     

Plasticity and limitations of extended egg retention in oviparous Zootoca vivipara (Reptilia: Lacertidae)

The transition between oviparity and viviparity in reptiles is generally accepted to be a gradual process, the result of selection for increasingly prolonged egg retention within the oviduct. We examined egg retention plasticity in an oviparous strain of the lacertid lizard Zootoca vivipara, a species having both oviparous and viviparous populations. We forced a group of female Z. vivipara to retain their clutch in utero by keeping them in dry substrata, and assessed the effect on embryonic development and hatching success, along with offspring phenotype and locomotor performance. Forced egg retention for one additional week affected the developmental stage of embryos at oviposition, as well as hatchling robustness and locomotor performance. However, embryos from forced clutch retention treatment reached one stage unit more than control embryos at oviposition time. Embryos from control eggs were more developed than embryos from experimental eggs after approximately the same period of external incubation, showing that embryonic development is retarded during the period of extended egg retention, despite the high temperature inside the mother's body. Significant differences in external incubation time were only found in one of the two years of study. Hatching success was much lower in the experimental group with forced egg retention (21.1%) than in the control group (95.4%). Therefore, we conclude that there are limitations that hinder the advance of intrauterine embryonic development beyond the normal time of oviposition, and that extended egg retention does not represent clear advantages in this population of Z. vivipara. Nevertheless, the fact that some eggs are successful after forced egg retention could be advantageous for the females that are able to retain their clutch under unfavourable climatic conditions. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 75–82.     

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.     

Food consumption,assimilation and rate of food passage in the cape rock elephant shrew,Elephantulus edwardii (macroscelidea: Macroscelidinae)

• 1.1. Food consumption, assimilation and passage rates of an elephant shrew, Elephantulus edwardii, on three natural diets (cockroaches, locusts and termites) and one artificial cereal diet (Pronutro) were compared.
• 2.2. Daily food consumption varies significantly between the diets and was partly related to % assimilation, which was highest on Pronutro and cockroaches (71%) and lowest on termites (31%).
• 3.3. Throughput times were estimated using soluble (⁵¹ Cr-EDTA) and particulate markers in the Pronutro diet. First appearance of the soluble marker (0.5 hr) was significantly earlier than for the particulate marker (1.85 hr); 50% appeared at 3.2 and 3.35 hr for the soluble and particulate markers, respectively.
• 4.4. The distribution of particulate markers in the digestive tract showed some retention in the stomach, ileum and colon, but rapid movement through the duodenum and very little entry to the caecum.

     

中国干旱半干旱区荒漠植物叶片(或同化枝)表皮微形态特征

为了探讨荒漠植物叶片表皮微形态结构对长期荒漠环境的适应特征及其分类学意义, 应用扫描电镜对中国干旱半干旱荒漠区28科74属117种200多个自然居群的植物叶片(或同化枝)表皮微形态进行了研究。荒漠植物叶(或同化枝)表皮的基本特征是: 表皮附属物相当丰富, 包括大量的表皮绒毛、角质膜蜡质片层或晶体颗粒、表面瘤状或疣状突起以及相对下陷且密度较低的气孔器。对表皮微形态结构及附属物组成进行对比分析, 将荒漠植物粗分为11种基本类型, 包括表皮完全被形态各异的蜡质层或表皮毛覆盖、不同形态类型的表皮毛和蜡质层结合、蜡质层与不同分布类型的气孔器或表皮毛结合, 以及各种突起的表皮细胞与蜡质层的结合等。根据抗逆所依赖的表皮及其附属物微形态结构, 将荒漠植物适应环境胁迫的叶片表皮微形态分为6种主要类型, 它们分别依赖于表皮毛、角质层蜡质、表皮凹凸结构、表面突起、混生的附属物以及上下表皮异化特征。荒漠植物叶表皮微形态结构的适应特征是通过表皮附属物(绒毛和角质膜蜡质层)与表皮结构(凹凸、乳突和气孔器)的相互协调作用, 共同抵御强光、降低叶片的蒸腾来提高植物对干旱等不利环境的抗性。该研究在一定程度上阐明了荒漠植物对逆境的适应机理及其演化趋势, 并为优良固沙植物的筛选提供了理论依据。     

Tree-rings and transportation in the New Zealand kauri (Agathis australis) timber industry: Investigating the time lag from tree to building

The interpretation of felling dates established by dendrochronological dating requires understanding of sample context and building practices, as well as knowledge of processes and timescales within the timber supply chain. In New Zealand (N.Z.), tree ring analysis of kauri from colonial-era (1840–1906) and early Dominion-era (1907–1920) buildings has been undertaken since 2000 and felling dates have been identified from several structures, providing a terminus post quem date for construction or modification of the building. What has been lacking is a good understanding of how long it took for a kauri tree to become timber used in a building or other structure. As a first estimate, felling dates from a small set of buildings were compared to documented construction dates, suggesting a delay of up to 5 years. To improve interpretation of felling dates, we investigated timescales associated with two stages of timber production within the 19th and early 20th century kauri timber industry: (a) transportation from stump to mill, and (b) seasoning of sawn timber. Documentary sources for ∼1850 until the 1920s were analysed, covering the development, expansion and decline of industrialised kauri timber production. The available evidence suggests that transportation to the sawmill was the most important variable. Logs could arrive within a few weeks of felling or potentially experience a delay of a year or more. Transportation times were affected by geography, weather, spatial differences and temporal changes in transportation methods and economic fluctuations. Seasoning of sawn timber probably contributed little to the time lag, as the balance of evidence suggests framing timber was not usually seasoned. In general, any delay associated with transportation and seasoning is unlikely to be more than a couple of years. The findings support the earlier use-date range of up to 5 years, but suggest it is generous. The dating of waney-edge timbers from buildings with accurate construction dates would help refine a use date range for kauri, as would further research into other stages of the production process including conversion of logs, transportation to market, and stockpiling in the timber yard and/or building site. The current study is also a starting point for further research in three related areas: (a) biography of timber; (b) technological change; and (c) trade networks.     

Aspects of dietary quality,nutrient assimilation and water balance in wild howler monkeys (Alouatta palliata)

Summary Wild howler monkeys were fed natural fruit and leaf diets in order to determine their ability to assimilate minerals (Ca, P, Mg, Si, Sr, Ba, Fe, Al, Mn, B, Cu, Li, V), and to assess their water and electrolyte budgets by the balance method. Results were extrapolated to the field situation so that the nutritional status of free-living monkeys could be examined in relation to their diet. The figs and young leaves of Ficus insipida and F. yoponensis trees (the most important foods in the dry season) provide adequate amounts of most required minerals, and an abundance of water. However, the copper requirement would not be met by this diet, which also provides only marginal amounts of sodium and phosphorus. These deficiencies may be corrected by consuming other available food items that are rich in Cu, Na or P. These results help explain the diversity that has been observed in the diet of wild howler monkeys, and suggest that these herbivores should feed selectively in order to obtain a nutritionally adequate diet.     

热耐受性及温度对食物同化的影响

研究变色树蜥(Calotes versicolor)的选择体温、热耐受性、温度对食物同化的影响.结果显示:①幼体的选择体温、临界高温和临界低温的平均值分别为32.6、41.7℃和 7.7℃;成体的选择体温、临界高温和临界低温的平均值分别为33.1、42.0℃和8.2℃.②环境温度在26～34℃时,对变色树蜥食物通过时间和摄入能有显著的影响;对表观消化系数(ADC)和同化效率(AE)无显著的影响;在28～34℃时食物通过时间随温度升高而缩短;在26、28℃和30℃时,摄入能小于更高温度的对应值.     

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.