Plasticity in food assimilation,retention time and coprophagy allow herbivorous cavies (Microcavia australis) to cope with low food quality in the Monte desert

Energy balance depends on the efficiency with which organisms make use of their trophic resources, and has direct impact on their fitness. There are environmental variations that affect the availability as well as the quality of such resources; energy extraction also depends on the design of the digestive tract. It is expected that features associated with food utilization will be subjected to selective pressures and show some adjustment to the variability of the environment. Since energetic constraints challenge animals to display digestive compensatory mechanisms, the objective of this study is to determine the physiological and behavioral responses to spatial and seasonal heterogeneity in food quality. We investigated digestive strategies (digestive efficiency and coprophagy) in cavies inhabiting two different populations, and hence naturally experiencing different levels of diet quality. Cavies under experimentally different quality diets showed changes in dry matter digestibility and intake, digesta retention time and coprophagy. Our results partially support the expectations from theory and also reveal interpopulation differences in the ability to cope with changes in food quality, and may explain the capability of Microcavia australis to colonize extreme habitats.     

Aerial and soil seed banks enable populations of an annual species to cope with an unpredictable dune ecosystem

Background and Aims

Simultaneous formation of aerial and soil seed banks by a species provides a mechanism for population maintenance in unpredictable environments. Eolian activity greatly affects growth and regeneration of plants in a sand dune system, but we know little about the difference in the contributions of these two seed banks to population dynamics in sand dunes.

Methods

Seed release, germination, seedling emergence and survival of a desert annual, Agriophyllum squarrosum (Chenopodiaceae), inhabiting the Ordos Sandland in China, were determined in order to explore the different functions of the aerial and soil seed banks.

Key Results

The size of the aerial seed bank was higher than that of the soil seed bank throughout the growing season. Seed release was positively related to wind velocity. Compared with the soil seed bank, seed germination from the aerial seed bank was lower at low temperature (5/15 °C night/day) but higher in the light. Seedling emergence from the soil seed bank was earlier than that from the aerial seed bank. Early-emerged (15 April–15 May) seedlings died due to frost, but seedlings that emerged during the following months survived to reproduce successfully.

Conclusions

The timing of seed release and different germination behaviour resulted in a temporal heterogeneity of seedling emergence and establishment between the two seed banks. The study suggests that a bet-hedging strategy for the two seed banks enables A. squarrosum populations to cope successfully with the unpredictable desert environment.     

A primer for data assimilation with ecological models using Markov Chain Monte Carlo (MCMC)

Data assimilation, or the fusion of a mathematical model with ecological data, is rapidly expanding knowledge of ecological systems across multiple spatial and temporal scales. As the amount of ecological data available to a broader audience increases, quantitative proficiency with data assimilation tools and techniques will be an essential skill for ecological analysis in this data-rich era. We provide a data assimilation primer for the novice user by (1) reviewing data assimilation terminology and methodology, (2) showcasing a variety of data assimilation studies across the ecological, environmental, and atmospheric sciences with the aim of gaining an understanding of potential applications of data assimilation, and (3) applying data assimilation in specific ecological examples to determine the components of net ecosystem carbon uptake in a forest and also the population dynamics of the mayfly (Hexagenia limbata, Serville). The review and examples are then used to provide guiding principles to newly proficient data assimilation practitioners.     

Shielding disk position in intra-operative electron radiotherapy (IOERT): A Monte Carlo study

PurposeIn IOERT breast treatments, a shielding disk is frequently used to protect the underlying healthy structures. The disk is usually composed of two materials, a low-Z material intended to be oriented towards the beam and a high-Z material. As tissues are repositioned around the shield before treatment, the disk is no longer visible and its correct alignment with respect to the beam is guaranteed. This paper studies the dosimetric characteristics of four possible clinical positioning scenarios of the shielding disk. A new alignment method for the shielding disk in the beam is introduced. Finally, it suggests a new design for the shielding disk.MethodsAs the first step, the IOERT machine “Mobetron 1000” was modeled by using Monte Carlo simulation, tuning the MC model until an excellent match with the measured PDDs and profiles was achieved. Four possible shielding disk positioning scenarios were considered, determining the dosimetric impact. Furthermore, in our center, to prevent beam misalignment, we have developed a shielding disk equipped with guiding rods. Having ascertained a correct alignment between the disk and the beam, we can propose a new internal design of the shielding disk that can improve the dose distribution with a better coverage of the treated area.ResultsAll MC simulations were performed with a 12 MeV beam, the maximum energy of Mobetron 1000 and a 5.5 cm diameter flat tip applicator, this applicator being the most clinically used. The simulations were compared with measurements performed in a water phantom and showed good results within 2.2% of root mean square difference (RMSD). The misplacement positions of the shielding disk have dosimetric impacts in the treatment volume and a small translation could have a significant influence on healthy tissues. The D-scenario is the worst which could happens when the shielding disk is flipped upside down, giving up to 144% dose instead of 90% at the surface of the Pb/Al shielding disk. A new shielding design used, together with our alignment tool, is able to give a more homogeneous dose in the target area.ConclusionsThe accuracy of shielding disk position can still be problematic in IOERT dosimetry. Any method that can ascertain the good alignment between the shielding disk and the beam is beneficial for the dose distribution and is a prerequisite for an optimized shield internal design that could improve the coverage of the treated area and the protection of healthy tissues.     

Conserving plant species with extremely small populations (PSESP) in China

Over the past decades, biodiversity conservation in China has achieved a number of successes. However, due to inadequate conservation policies, poor implementation and lack of financial support, wild plant species that are extremely small in population size and therefore seriously threatened have not had the attention they require. But the new concept of plant species with extremely small populations (PSESP), first promulgated in Yunnan Province, is becoming more widely accepted in China. Several national and regional-level conservation strategies and actions for conserving China’s PSESP are being implemented over the next 5 years. With this new policy framework leading the way, plant conservation in China is set to make important new advances.     

Plant species with extremely small populations (PSESP) in China: A seed and spore biology perspective

Approximately one fifth of the world's plants are at risk of extinction. Of these, a significant number exist as populations of few individuals, with limited distribution ranges and under enormous pressure due to habitat destruction. In China, these most-at-risk species are described as ‘plant species with extremely small populations’ (PSESP). Implementing conservation action for such listed species is urgent. Storing seeds is one of the main means of ex situ conservation for flowering plants. Spore storage could provide a simple and economical method for fern ex situ conservation. Seed and spore germination in nature is a critical step in species regeneration and thus in situ conservation. But what is known about the seed and spore biology (storage and germination) of at-risk species? We have used China's PSESP (the first group listing) as a case study to understand the gaps in knowledge on propagule biology of threatened plant species. We found that whilst germination information is available for 28 species (23% of PSESP), storage characteristics are only known for 8% of PSESP (10 species). Moreover, we estimate that 60% of the listed species may require cryopreservation for long-term storage. We conclude that comparative biology studies are urgently needed on the world's most threatened taxa so that conservation action can progress beyond species listing.     

论极小种群野生植物的研究及科学保护

<正>近年来,中国在生物多样性保护方面取得了一系列成就,但由于人类对自然资源的不断索取和全球变化,一些野生植物仍面临灭绝的风险。目前,仅有1999年国务院批准的《国家重点保护野生植物名录(第一批)》所列种类受到法律的保护。早在20世纪80年代,我国就引入国际自然保护联盟(IUCN)红色名录的评估体系开展了受威胁物种的评估工作,先后出版了《中国植物红皮书:稀有濒危植物》(第一册)(傅立国,1991)和《中国物种红色名录》(汪     

Hypogynous bristles and scales in basal florets in amphicarpous Schoenoplectus species (Cyperaceae)

A perianth of bristles is known in both aerial and basal florets of the amphicarpous sedge Eleocharis minima. For the first time, a perianth is reported within basal florets of Schoenoplectus section Supini. Aerial florets of the same plants show no evidence of a perianth. In S. erectus ssp. raynalii and in S. lateriflorus ssp. lateriflorus , the perianth to the basal amphicarp consisted of two bristles with antrorse barbs. In S. articulatus, S. roylei and S. senegalensis the perianth comprised broader, smooth-margined structures interpreted as scales. In some cases these were three per floret and were set at two levels suggestive of two whorls. Other amphicarpous species of the section showed basal florets without a perianth.     

Kinetic Monte Carlo Predictions of the Conditions Necessary to Grow Helical (Chiral) and Vertical Columnar Structures

Abstract

Rare Event Dynamics Monte Carlo simulations have been used to investigate the possibility of growing porous crystalline material possessing vertical columnar morphology. This is achieved using a deposition process in which the incoming beam of atoms is held at a grazing angle and, importantly, is rotated azimuthally. For incident beams 80° from normal incidence, rotational speeds of around 1 revolution per second to 1 per 10 seconds were found to produce columnar thin film growth with essentially vertical walls. Slower rotational speeds, around 1 revolution per 30 seconds, produced a helical, but still vertical, columnar structure. Such so-called chiral structures are postulated to be potentially important optical materials. The effect of raising the temperature of the substrate is to decrease the density of the columns, but to broaden their size. This suggests that a temperature-rotational speed set of parameters could be found to produce designer pore sizes with relatively little variation in inter-column spacing and height and either with or without helical structure. Data for one such representation are presented. A movie of the evolution of the nanostructural features of a vertical columnar material is included.     

Contrasting strategies to cope with drought by invasive and endemic species of Lantana in Galapagos

This study compares how Lantana camara, an invasive species, and L. peduncularis, an autochthonous one, cope with drought in Galapagos. Soil surface temperature was the abiotic environmental parameter that best explained variations in photosynthetic stress. Higher soil surface temperatures were recorded in the lowlands and in rain-shadow areas, which were also the driest areas. L. peduncularis, with a shallow root system, behaved as a drought-tolerant species, showing lower relative growth rates, which decreased with leaf water content and higher photosynthetic stress levels in the lowlands and in a northwest rain-shadow area in comparison with higher and wetter locations. Its basal and maximal fluorescences decreased at lower altitudes, reflecting the recorded drops in chlorophyll concentration. In contrast, L. camara with a deep root system behaved as a drought-avoiding species, showing leaf and relative water contents higher than 55% and avoiding permanent damage to its photosynthetic apparatus even in the driest area where it showed very low chlorophyll content. Its relative growth rate decreased more in dry areas in comparison to wetter zones than did that of L. peduncularis, even though it had greater water content. Furthermore, L. camara showed higher water contents, growth rate, and lower photosynthetic stress levels than L. peduncularis in the arid lowlands. Thus, L. peduncularis maintained lower maximum quantum efficiency of photosystem II photochemistry (F _v/F _m) than L. camara even at sunrise, due to higher basal fluorescence values with similar maximal fluorescence, which indicated permanent damage to PSII reaction centres. Our results help to explain the success and limitations of L. camara in the invasion of arid and sub-arid environments.     

A hybrid swarm between two hummingbird-pollinated species of Columnea(Gesneriaceae) in Jamaica

A hybrid swarm between the hummingbird-pollinated Jamaican endemics Columnea urbanii Stearn and C. rutilans Swartz (Gesneriaceae) is described in terms of morphological, chemical and cytological characters.
The importance of man-made ecological niches to the establishment of hybrids is outlined and contrasted with the paucity of niches in undisturbed Columnea habitats. Niche availability determines the effectiveness of dissemination of both hybrid and pure seed.
With the variation pattern of the Jamaican hybrids in mind, the possibility of hybridization between columneas elsewhere should be considered in systematic assessment of difficult groups in the genus.     

中国大戟属13种15个居群的核型报道

对国产大戟科Euphorbiaceae大戟属Euphorbia的13种15个地方居群的核型进行研究, 以期为解决该属的种间亲缘关系和物种进化机制提供依据。结果如下: 地锦E. humifusa (望江居群), 2n=2x=22=20m (2SAT)+2sm; 地锦E. humifusa (红旗村居群), 2n=2x=22=18m+4sm; 千根草E. thymifolia, 2n=4x=40=40m; 斑地锦E. maculata, 2n=4x=40=36m+4sm; 银边翠E. marginata, 2n=8x=56=40m+ 8sm+8st; 铁海棠E. milii, 2n=4x=40=32m+8sm; 金刚纂E. neriifolia, 2n=6x=60=6m+36sm+12st+6t; 火殃勒E. antiquorum, 2n=6x=60=24m+24sm+12st; 一品红E. pulcherrima, 2n=4x=28=24m(3SAT)+4sm; 猩猩草E. cyathophora, 2n=4x=28=16m+12sm; 齿裂大戟E. dentata, 2n=4x=28=28m; 续随子E. lathyris, 2n=2x=20=12m+8sm; 泽漆E. helioscopia, 2n=6x=42=36m+6sm; 乳浆大戟E. esula (陈家沟居群), 2n=2x=20=14m+6sm; 乳浆大戟E. esula (樱桃沟居群), 2n=4x=40=32m+8sm。千根草和斑地锦两个种的核型以及乳浆大戟的四倍体居群核型均为首次报道。     

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology.

An unknown protein structure can be predicted with fair accuracy once an evolutionary connection at the sequence level has been made to a protein of known 3-D structure. In model building by homology, one typically starts with a backbone framework, rebuilds new loop regions, and replaces nonconserved side chains. Here, we use an extremely efficient Monte Carlo algorithm in rotamer space with simulated annealing and simple potential energy functions to optimize the packing of side chains on given backbone models. Optimized models are generated within minutes on a workstation, with reasonable accuracy (average of 81% side chain chi 1 dihedral angles correct in the cores of proteins determined at better than 2.5 A resolution). As expected, the quality of the models decreases with decreasing accuracy of backbone coordinates. If the back-bone was taken from a homologous rather than the same protein, about 70% side chain chi 1 angles were modeled correctly in the core in a case of strong homology and about 60% in a case of medium homology. The algorithm can be used in automated, fast, and reproducible model building by homology.     

Leaf traits in parental and hybrid species of Sorbus (Rosaceae)

? Premise of the study: Knowledge of functional leaf traits can provide important insights into the processes structuring plant communities. In the genus Sorbus, the generation of taxonomic novelty through reticulate evolution that gives rise to new microspecies is believed to be driven primarily by a series of interspecific hybridizations among closely related taxa. We tested hypotheses for dispersion of intermediacy across the leaf traits in Sorbus hybrids and for trait linkages with leaf area and specific leaf area. ? Methods: Here, we measured and compared the whole complex of growth, vascular, and ecophysiological leaf traits among parental (Sorbus aria, Sorbus aucuparia, Sorbus chamaemespilus) and natural hybrid (Sorbus montisalpae, Sorbus zuzanae) species growing under field conditions. A recently developed atomic force microscopy technique, PeakForce quantitative nanomechanical mapping, was used to characterize the topography of cell wall surfaces of tracheary elements and to map the reduced Young's modulus of elasticity. ? Key results: Intermediacy was associated predominantly with leaf growth traits, whereas vascular and ecophysiological traits were mainly parental-like and transgressive phenotypes. Larger-leaf species tended to have lower modulus of elasticity values for midrib tracheary element cell walls. Leaves with a biomass investment related to a higher specific leaf area had a lower density. Leaf area- and length-normalized theoretical hydraulic conductivity was related to leaf thickness. ? Conclusions: For the whole complex of examined leaf traits, hybrid microspecies were mosaics of parental-like, intermediate, and transgressive phenotypes. The high proportion of transgressive character expressions found in Sorbus hybrids implies that generation of extreme traits through transgressive segregation played a key role in the speciation process.     

Monte Carlo simulations and measurement of DNA damage from x-ray-triggered Auger cascades in iododeoxyuridine (IUdR)

We investigated the DNA damage from Auger electrons emitted from incorporated stable iodine (¹²⁷I), following photoelectric absorption of external x-rays. The effectiveness of the Auger electrons in producing DNA double-strand breaks (DSB) was determined theoretically, using Monte Carlo simulations of the radiation physics and chemistry, and was shown to be in reasonable agreement with DNA damage measured using the comet assay. The DSB yields were measured in CHO cells for ⁶⁰Co (as a non-Auger-promoting radiation) and for tungsten-filtered 100 kVp x-rays capable of producing Auger electron emission. The theoretical study showed that on average, 2.5 Auger electrons were emitted for N-shell orbital vacancies and up to 10 Auger electrons were emitted from L₁-shell vacancies. These Auger bursts produced approximately 0.03 DSB per N-shell vacancy and 0.3 DSB per K-shell or L-shell vacancy. The calculated yield of DSB from Auger cascades per unit dose (1 Gy) in water was approximately 1.7 for tungsten-filtered 100 kVp x-rays, assuming 20% IUdR substitution of thymidine. The comet assay yielded an experimental value of 3.6±1.6 per 1 Gy for the same conditions. The Monte Carlo simulations also demonstrated a high complexity of DSB produced by Auger cascades with virtually all DSB from inner shell orbitals (i.e. K, L shells) accompanied by compounded strand breakage and base damage, indicating a difficult lesion to repair. This finding agrees well with comet assay results of DNA repair, where an increase in the DSB yield in IUdR-sensitized cells was shown to persist after a time of 24 h. We conclude that Auger cascades in iodine produce a modest increase in the number of initial strand breaks of the order of 10% but the complex nature of these DSB makes them very difficult to repair or potentially prone to misrepair. The accentuated DNA damage may have major consequences for cell survival and may be exploitable in kilovoltage photon activation therapy (PAT) of tumors sensitized with iodine. Received: 23 October 2000 / Accepted: 26 March 2001     

An intracellular symbiont and other microbiota associated with field-collected populations of sawflies (Hymenoptera: Symphyta)

Six species of sawfly (Hymenoptera: Symphyta) from four taxonomic families (Agridae, Diprionidae, Pamphiliidae, and Tenthredinidae) were collected from locations across Canada and surveyed for their associated microbiota. Total DNA was extracted from individual insects, and polymerase chain reaction (PCR) was used to amplify the conserved 16S rRNA gene from microbiota. Denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were undertaken to separate bacterial clones associated with the host insect. Sequencing of the PCR-DGGE and PCR-RFLP products revealed a dominance of alpha- and gamma-Proteobacteria, with most sequences showing high similarity to bacteria previously identified from other insect species and environmental samples. Additionally, a strain of the bacterial endosymbiont Wolbachia and a Wolbachia bacteriophage were identified from the mountain ash sawfly (Pristiphora geniculata).     

A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: comparison with crystallographic ordered water sites

Monte Carlo computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one- and two-water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x-ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and ammonium salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation to compete unfavorably with the adjacent donor site at guanine N2. There is, however, a significant probability of finding a one-water G-N3-W-G-N2 bridge indicated in the simulation. An explanation for the guanine N3 discrepancy in terms of electrostatic potentials is also offered. The calculated one- and two-water bridges in the rGpC hydration complex coincide in a number of cases to those observed in the ordered water structure of the sodium rGpC crystal hydrate.     

Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions

Mathematical models have substantially improved our ability to predict the response of a complex biological system to perturbation, but their use is typically limited by difficulties in specifying model topology and parameter values. Additionally, incorporating entities across different biological scales ranging from molecular to organismal in the same model is not trivial. Here, we present a framework called "querying quantitative logic models" (Q2LM) for building and asking questions of constrained fuzzy logic (cFL) models. cFL is a recently developed modeling formalism that uses logic gates to describe influences among entities, with transfer functions to describe quantitative dependencies. Q2LM does not rely on dedicated data to train the parameters of the transfer functions, and it permits straight-forward incorporation of entities at multiple biological scales. The Q2LM framework can be employed to ask questions such as: Which therapeutic perturbations accomplish a designated goal, and under what environmental conditions will these perturbations be effective? We demonstrate the utility of this framework for generating testable hypotheses in two examples: (i) a intracellular signaling network model; and (ii) a model for pharmacokinetics and pharmacodynamics of cell-cytokine interactions; in the latter, we validate hypotheses concerning molecular design of granulocyte colony stimulating factor.