Peristaltic motion of Phan–Thien–Tanner fluid in the presence of slip condition

This investigation considers the peristaltic flow of a Phan–Thien–Tanner fluid in the presence of slip condition and induced magnetic field. By use of the long wavelength and low Reynolds number approximations, closed form series solutions for stream function, pressure gradient, magnetic force function, axial induced magnetic field, and current density were obtained. The pressure gradient and frictional forces per wavelength were computed by numerical integration. The velocity slip condition in terms of shear stress is taken into account. Graphical results show the comparison between no-slip and viscous fluid cases. Pumping and trapping phenomena are discussed.     

Revisiting Beverton–Holt recruitment in the presence of variation in food availability

Understanding density-dependent changes in juvenile survival and growth rates is of great importance because these rates determine recovery rates for imperiled populations and/or sustainable harvest rates. Unfortunately, the mechanisms leading to density dependent survival and growth are among the least understood process in biology and fisheries. Previous work has shown that small fish may vary foraging times to achieve a target growth rate, resulting in the well-known Beverton–Holt recruitment function with variation in food availability affected the initial slope of the recruitment curve. We amend their derivation to show that incorporating fish growth under a variety of evolutionary strategies for balancing foraging time and predation risk still leads to recruitment approximately as expected under the Beverton–Holt recruitment model but that changing food availability affects both the initial slope and maximum recruitment level. We demonstrate that when food availability is known to vary over time, these models often result in a more parsimonious alternative than the standard Beverton–Holt function. Further, Beverton–Holt recruitment is expected when foraging times are adjusted to balance fitness gains from growth against mortality risk. Finally, linking recruitment success to food availability warns that species with high scope for density dependent survival (high compensation ratio or steepness) may be extremely sensitive to changes in available food densities. This work emphasizes the sensitivity of stock-recruitment parameters to food availability and strongly suggests a need to carefully monitor lower trophic levels to better understand and predict dramatic changes in juvenile recruitment and carrying capacity.     

Structure and ecological function of the soil microbiome affecting plant–soil feedbacks in the presence of a soil-borne pathogen

Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.     

Transglycosylation of a β-galactosyl radical, in the course of enzymic hydrolysis of lactose, in the presence of selected polyhydroxyalcohols

Sorbitol, xylitol, erythritol and lactitol were used as the acceptors of galactosyl radicals, in the process of transgalactosylation accompanying the hydrolysis of lactose, conducted with -galactosidase (4.0 ml Lactozym 3000 was added to 430 ml 1.45 M lactose with 0.95 M polyhydroxyalcohols). The following concentrations of galactosyl derivatives of polyols were obtained after hydrolysis for 4 h at 40°C: 0.31 M Gal-erythritol, 0.22 M Gal-xylitol, 0.18 M Gal-sorbitol and 0.14 M Gal-lactitol. A quadruple increase of xylitol content in dry matter of a solution (from 11.5% (w/w) to 44.5% (w/w) brought about a 2.3-fold increase of the product content in the solution (15.2% (w/w) of dry matter).     

Density of tiger and leopard in a tropical deciduous forest of Mudumalai Tiger Reserve,southern India,as estimated using photographic capture–recapture sampling

Density of tiger Panthera tigris and leopard Panthera pardus was estimated using photographic capture–recapture sampling in a tropical deciduous forest of Mudumalai Tiger Reserve, southern India, from November 2008 to February 2009. A total of 2,000 camera trap nights for 100 days yielded 19 tigers and 29 leopards within an intensive sampling area of 107 km². Population size of tiger from closed population estimator model M_b Zippin was 19 tigers (SE = ±0.9) and for leopards M_h Jackknife estimated 53 (SE = ±11) individuals. Spatially explicit maximum likelihood and Bayesian model estimates were 8.31 (SE = ±2.73) and 8.9 (SE = ±2.56) per 100 km² for tigers and 13.17 (SE = ±3.15) and 13.01 (SE = ±2.31) per 100 km² for leopards, respectively. Tiger density for MMDM models ranged from 6.07 (SE = ±1.74) to 9.72 (SE = ±2.94) per 100 km² and leopard density ranged from 13.41 (SE = ±2.67) to 28.91 (SE = ±7.22) per 100 km². Spatially explicit models were more appropriate as they handle information at capture locations in a more specific manner than some generalizations assumed in the classical approach. Results revealed high density of tiger and leopard in Mudumalai which is unusual for other high density tiger areas. The tiger population in Mudumalai is a part of the largest population at present in India and a source for the surrounding Reserved Forest.     

Wildfire occurrence in forests of the Altai–Sayan region under current climate changes

The dynamics of meteorological parameters in Siberia and the Altai–Sayan region in the 20^th–21^st centuries are analyzed. Significant trends characterizing the dynamics of the average temperature, precipitation, and standardized precipitation evapotranspiration index (SPEI) are revealed. Growing wildfire frequency in the area under study since the end of the 20^th century has been detected. The annual variation of wildfires has a phase coincidence with the dynamics of mean temperatures, positively correlates with climate dryness, and negatively correlates with averaged precipitation data. An abrupt increase in wildfire frequency has been observed in the late 20^th–early 21^st centuries. The spatial redistribution of wildfires in the Altai–Sayan region in the early 21^st century is revealed.     

Methylation of methyl α-d-hexopyranosides with diazo-methane in the presence of a small amount of water

The long-time reduction of methyl α-d-gluco-, α-d-manno-, and α-d-galactopyranosides with excess diazomethane-diethyl ether at 25° in the presence of water gave all partially methylated methyl α-d-hexopyranosides which differ in number and position of methyl substitution. The presence of electrolytes, such as potassium or sodium phosphate, in the reaction medium enhanced the degree of methylation, resulting in preferential formation of tri-O-methyl derivatives of methyl α-d-hexopyranosides.     

Predator–prey interactions in anurans of the tropical dry forests of the Colombian Caribbean: A functional approach

Anuran–prey selection might be mediated by traits, either by mismatches in predator and prey traits (preventing interactions) or by predator selection of prey traits (encouraging interactions). These effect traits could be summarized in two contrasting foraging strategies: “active” and “sit-and-wait” foragers. We evaluated whether anurans could be classified into groups of species sharing traits associated with their diet, and what is the relation between particular effect traits of anurans and their prey. We collected anurans and identified their stomach contents once during dry, minor, and major rain seasons in six dry forest sites in the Colombian Caribbean. For each of the 19 anuran species and 436 prey items, we registered six effect traits. We applied RLQ and fourth-corner methodologies to relate predator and prey traits through their interaction matrix. Predators were assigned to five groups according to their differences in locomotion, body shape, proportion of the jaw width, mode of tongue protrusion, and strata preferred. Regarding preys, species were assigned to four groups according to their gregariousness, body shape and hardness, defensive traits, and mobility. Body size of both, predators and prey, had a minor contribution in the group assignment. We found that predators using active search target low-mobility preys, whereas species using sit-and-wait strategy target highly nutritive prey that are difficult to manipulate. By linking amphibian diet with foraging strategies, we hope to contribute to the understanding of mechanisms behind anuran–prey food web patterns and to build more realistic models of functional response to changing environments.     

Bayesian latent class models for capture–recapture in the presence of missing data

We propose a method for estimating the size of a population in a multiple record system in the presence of missing data. The method is based on a latent class model where the parameters and the latent structure are estimated using a Gibbs sampler. The proposed approach is illustrated through the analysis of a data set already known in the literature, which consists of five registrations of neural tube defects.     

Templates of food–habitat resources for the organization of soil animals in temperate and tropical forests

The functioning and structure of terrestrial ecosystems are shaped and maintained by plant–decomposer interactions. The food and habitat of animal populations are biogenic and are mainly of plant origin (plant litter) in terrestrial ecosystems. Primary resources of the food-habitat template for the organization of soil animals are provided by the primary production of plants, and are then modified through decomposition processes by microbial populations. In the microbial decomposition system, the efficiency of carbon utilization by microbial decomposers characterizes the decomposition processes between tropical and temperate forest ecosystems. Tropical forests show poor development of soil reservoir systems because of the high efficiency of lignin decomposition by microbial populations. The decomposition processes of leaf litter are described briefly for the understanding of organization of soil animal communities in tropical and temperate forests. A comparison of decomposition processes shows qualitative differences in decomposition between temperate and tropical forests. The composition of functional groups of soil animals is well explained by the decomposition processes in both forests.     

Extinction–immigration dynamics lag behind environmental filtering in shaping the composition of tropical dry forests within a changing landscape

The impact of rapid habitat loss and fragmentation on biodiversity is a major issue. However, we still lack an integrative understanding of how these changes influence biodiversity dynamics over time. In this study, we investigate the effects of these changes in terms of both niche-based and neutral dynamics. We hypothesize that habitat loss has delayed effects on neutral immigration–extinction dynamics, while edge effects and environmental heterogeneity in habitat patches have rapid effects on niche-based dynamics. We analyzed taxonomic and functional composition of 100 tree communities in a tropical dry forest landscape of New-Caledonia subject to habitat loss and fragmentation. We designed an original, process-based simulation framework, and performed Approximate Bayesian Computation to infer the influence of niche-based and neutral processes. Then, we performed partial regressions to evaluate the relationships between inferred parameter values of communities and landscape metrics (distance to edge, patch area, and habitat amount around communities), derived from either recent or past (65 yr ago) aerial photographs, while controlling for the effect of soil and topography. We found that landscape structure influences both environmental filtering and immigration. Immigration rate was positively related to past habitat amount surrounding communities. In contrast, environmental filtering was mostly affected by present landscape structure and mainly influenced by edge vicinity and topography. Our results highlight that landscape changes have contrasting spatio-temporal influences on niche-based and neutral assembly dynamics. First, landscape-level habitat loss and community isolation reduce immigration and increase demographic stochasticity, resulting in slow decline of local species diversity and extinction debt. Second, recent edge creation affects environmental filtering, incurring rapid changes in community composition by favoring species with edge-adapted strategies. Our study brings new insights about temporal impacts of landscape changes on biodiversity dynamics. We stress that landscape history critically influences these dynamics and should be taken into account in conservation policies.     

Evidence for the presence of a critical disulfide bond in the mouse EP3γ receptor

To determine the contribution of cysteines to the function of the mouse E-prostanoid subtype 3 gamma (mEP3γ), we tested a series of cysteine-to-alanine mutants. Two of these mutants, C107A and C184A, showed no agonist-dependent activation in a cell-based reporter assay for mEP3γ, whereas none of the other cysteine-to-alanine mutations disrupted mEP3γ signal transduction. Total cell membranes prepared from HEK293 cells transfected with mEP3γ C107A or C184A had no detectable radioligand binding. Other mutant mEP3γ receptors had radioligand affinities and receptor densities similar to wild-type. Cell-surface ELISA against the N-terminal HA-tag of C107A and C184A demonstrated 40% and 47% reductions respectively in receptor protein expression at the cell surface, and no radioligand binding was detected as assessed by intact cell radioligand binding experiments. These data suggest a key role for C107 and C184 in both receptor structure/stability and function and is consistent with the presence of a conserved disulfide bond between C107 and C184 in mouse EP3 that is required for normal receptor expression and function. Our results also indicate that if a second disulfide bond is present in the native receptor it is non-essential for receptor assembly or function.     

Large-scale synchrony of gap dynamics and the distribution of understory tree species in maple–beech forests

Large-scale synchronous variations in community dynamics are well documented for a vast array of organisms, but are considerably less understood for forest trees. Because of temporal variations in canopy gap dynamics, forest communities—even old-growth ones—are never at equilibrium at the stand scale. This paucity of equilibrium may also be true at the regional scale. Our objectives were to determine (1) if nonequilibrium dynamics caused by temporal variations in the formation of canopy gaps are regionally synchronized, and (2) if spatiotemporal variations in canopy gap formation affect the relative abundance of tree species in the understory. We examined these questions by analyzing variations in the suppression and release history of Acer saccharum Marsh. and Fagus grandifolia Ehrh. from 481 growth series of understory saplings taken from 34 mature stands. We observed that (1) the proportion of stems in release as a function of time exhibited a U-shaped pattern over the last 35 years, with the lowest levels occurring during 1975–1985, and that (2) the response to this in terms of species composition was that A. saccharum became more abundant at sites that had the highest proportion of stems in release during 1975–1985. We concluded that the understory dynamics, typically thought of as a stand-scale process, may be regionally synchronized.     

Vegetation changes in forests of the Krkonoše Mts. over a period of air pollution stress (1980–1995)

Species composition of the understory of spruce (Picea abies (L.) Karsten) and beech (Fagus sylvatica L.) forests subjected to intense air pollution stress in the Krkonoe Mts., Czech Republic, showed directional changes over the last 15 years. The changes were documented with repeated observations of 29 permanent plots, initiated in 1980 and analysed with constrained ordination methods (Canonical Correspondence Analysis). Ground layer changes were mainly associated with the loss of canopy foliage from air pollution stress. The increased amount of the light at ground level resulted in increased herb cover. The initially dominant species (e.g., Calamagrostis villosa (Chaix) J. F. Gmelin, Deschampsia flexuosa (L.) P. B., Vaccinium myrtillus L., Athyrium distentifolium Tausch) were those that increased in cover. Moss cover, and moss and herb richness, declined over the course of the study. Thus, the changes in tree canopy are accompanied with changes in the forest understory, which in turn can affect the dynamics of these forests.     

Properties of Jack bean α-mannosidase in the presence of hyaluronan

An enzymatic reaction within a mesh-like structure constructed using hyaluronan was investigated in order to understand the influence of specific reaction environments in a living body on the reaction. This mesh-like structure, which mimicked extracellular matrix conditions, was found to accelerate glycohydrolysis by Jack bean α-mannosidase.     

Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction–modification enzyme

EcoP15I is a Type III DNA restriction and modification enzyme of Escherichia coli. We show that it contains two modification (Mod) subunits for sequence-specific methylation of DNA and one copy of a restriction endonuclease (Res) subunit for cleavage of DNA containing unmethylated target sequences. Previously the Mod₂ dimer in the presence of cofactors was shown to use nucleotide flipping to gain access to the adenine base targeted for methylation (Reddy and Rao, J. Mol. Biol. 298 (2000) 597–610.). Surprisingly the Mod₂ enzyme also appeared to flip a second adenine in the target sequence, one which was not subject to methylation. We show using fluorescence lifetime measurements of the adenine analogue, 2-aminopurine, that only the methylatable adenine undergoes flipping by the complete Res₁Mod₂ enzyme and that this occurs even in the absence of cofactors. We suggest that this is due to activation of the Mod₂ core by the Res subunit.     

Behaviour of α-aminoadipylcysteine and glutamylcysteine in the presence of intact and disrupted mycelium of a Cephalosporium sp

1. delta-(l-alpha-Aminoadipyl)-l-cysteine, the corresponding d- and dl-alpha-aminoadipyl isomers, delta-(dl-alpha-amino[6-(14)C]adipyl)-l-cysteine and gamma- and alpha-l-glutamyl-l-cysteine were synthesized. 2. The behaviour of delta-(l-aminoadipyl)-l-cysteine and the corresponding d- and dl-alpha-aminoadipyl isomers was studied in the presence of suspensions of intact mycelium of a Cephalosporium sp., suspensions treated ultrasonically and extracts obtained by grinding with alumina. 3. With intact mycelium the l-alpha-aminoadipyl isomer was removed more rapidly from the extracellular fluid than the corresponding d-isomer. 4. Addition of delta-(dl-alpha-amino[6-(14)C]adipyl)-l-cysteine to suspensions of intact mycelium led to the labelling of extracellular and intracellular penicillin N and cephalosporin C, but also to extensive hydrolysis of the dipeptide. 5. Broken-cell systems hydrolysed delta-(l-alpha-aminoadipyl)-l-cysteine and the corresponding d-alpha-aminoadipyl isomer, but the former was hydrolysed more readily than the latter. 6. gamma- and alpha-l-Glutamyl-l-cysteine were also hydrolysed but delta-(l-alpha-aminoadipyl)-l-cysteinyl-l-valine was not. 7. Only part of the enzyme activity in broken-cell systems responsible for the hydrolysis of delta-(alpha-aminoadipyl)-l-cysteine was present in the supernatant obtained on centrifugation at 20000g. 8. Possible implications of these findings are discussed.     

Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate “evolutionarily significant unit” (ESU) following the adaptive evolutionary conservation (AEC) concept.