On the best partitioning of the density functional energy

This essay discusses special features for two different ways of partitioning the density functional energy expression. The contribution, which is part of the special issue for Pratim Chattaraj, was stimulated by a thought-provoking suggestion by him at a recent conference.     

The generalized replication principle and the partitioning of functional diversity into independent alpha and beta components

The replication principle was first proposed by Hill (1973, Ecology 54: 247– 432) as an advantageous property of his family of diversity indices. Later Jost (2007, Ecology 88: 2427– 2439) discovered that diversity measures satisfying this principle allow partitioning of gamma diversity into independent alpha and beta components by simple multiplicative partitioning. Despite the emerging agreement on measuring taxonomic beta‐diversity by multiplicative partitioning of Hill diversity, there is no consensus on how to measure functional beta diversity. Two different generalizations of Hill numbers for measuring functional diversity were proposed by Leinster and Cobbold (2011, Ecology 93: 477– 489) and Chiu and Chao (2014, PLoS One 9: e1000014). Both generalizations attempted to satisfy the generalized replication principle, but they formulate it in different ways. The aims of this paper are 1) to review approaches for measuring functional diversity in units of equivalent numbers without explicit reference to replication principle; 2) to compare the two proposed replication principle and to point out some important differences in the behavior of diversity families derived from the two principles; 3) to explore the conditions necessary for partitioning functional diversity of Leinster and Cobbold into meaningful alpha and beta components; 4) and, finally, to explore how transformation of among‐species distances into similarities influences the sensitivity of functional diversity to the scale parameter.     

Assembly rules for functional groups of North American shrews: effects of geographic range and habitat partitioning

Trophic cascades exist in numerous terrestrial systems, including many systems with ants as the top predator. Many studies show how behavioral modifications of herbivores are especially important in mediating species interactions and trophic cascades. Although most studies of trophic cascades focus on predator-herbivore-plant links, the trophic cascades concept could be applied to almost any level of trophic interactions. Especially considering the importance of parasites we consider here the interactions between the parasitic phorid fly, Pseudacteon sp. (Diptera: Phoridae), its ant host, Azteca instabilis (F. Smith) (Hymenoptera: Formicidae), and the herbivore, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) in the coffee agroecosystem. We investigated the effects of phorid flies on ant behavior by monitoring ant recruitment to tuna baits over a 30-min period in the presence or absence of phorid flies. To study the indirect effects of phorids on larvae, we placed baits on coffee plants to elevate ant foraging levels to levels near to ant nests, placed larvae near baits, and recorded the effects of ants on larvae either in the presence or absence of phorid flies. We found that phorid fly presence significantly reduced ant ability to recruit to baits through behavioral modifications and also significantly lessened ant ability to attack, carry away, or force herbivores off plants. We conclude there is a behaviorally-modified species-level trophic cascade in the coffee agroecosystem, with potentially important effects in ant and herbivore communities as well as for coffee production.     

A novel Bayesian functional spatial partitioning method with application to prostate cancer lesion detection using MRI

Spatial partitioning methods correct for nonstationarity in spatially related data by partitioning the space into regions of local stationarity. Existing spatial partitioning methods can only estimate linear partitioning boundaries. This is inadequate for detecting an arbitrarily shaped anomalous spatial region within a larger area. We propose a novel Bayesian functional spatial partitioning (BFSP) algorithm, which estimates closed curves that act as partitioning boundaries around anomalous regions of data with a distinct distribution or spatial process. Our method utilizes transitions between a fixed Cartesian and moving polar coordinate system to model the smooth boundary curves using functional estimation tools. Using adaptive Metropolis-Hastings, the BFSP algorithm simultaneously estimates the partitioning boundary and the parameters of the spatial distributions within each region. Through simulation we show that our method is robust to shape of the target zone and region-specific spatial processes. We illustrate our method through the detection of prostate cancer lesions using magnetic resonance imaging.     

Maintenance of the virulence plasmid in Shigella flexneri is influenced by Lon and two functional partitioning systems

Members of the genus Shigella carry a large plasmid, pINV, which is essential for virulence. In Shigella flexneri, pINV harbours three toxin‐antitoxin (TA) systems, CcdAB, GmvAT and VapBC that promote vertical transmission of the plasmid. Type II TA systems, such as those on pINV, consist of a toxic protein and protein antitoxin. Selective degradation of the antitoxin by proteases leads to the unopposed action of the toxin once genes encoding a TA system have been lost, such as following failure to inherit a plasmid harbouring a TA system. Here, we investigate the role of proteases in the function of the pINV TA systems and demonstrate that Lon, but not ClpP, is required for their activity during plasmid stability. This provides the first evidence that acetyltransferase family TA systems, such as GmvAT, can be regulated by Lon. Interestingly, S. flexneri pINV also harbours two putative partitioning systems, ParAB and StbAB. We show that both systems are functional for plasmid maintenance although their activity is masked by other systems on pINV. Using a model vector based on the pINV replicon, we observe temperature‐dependent differences between the two partitioning systems that contribute to our understanding of the maintenance of virulence in Shigella species.     

KV10.1 K+-channel plasma membrane discrete domain partitioning and its functional correlation in neurons

K_V10.1 potassium channels are implicated in a variety of cellular processes including cell proliferation and tumour progression. Their expression in over 70% of human tumours makes them an attractive diagnostic and therapeutic target. Although their physiological role in the central nervous system is not yet fully understood, advances in their precise cell localization will contribute to the understanding of their interactions and function. We have determined the plasma membrane (PM) distribution of the K_V10.1 protein in an enriched mouse brain PM fraction and its association with cholesterol- and sphingolipid-rich domains. We show that the K_V10.1 channel has two different populations in a 3:2 ratio, one associated to and another excluded from Detergent Resistant Membranes (DRMs). This distribution of K_V10.1 in isolated PM is cholesterol- and cytoskeleton-dependent since alteration of those factors changes the relationship to 1:4. In transfected HEK-293 cells with a mutant unable to bind Ca^2 +/CaM to K_V10.1 protein, Kv10.1 distribution in DRM/non-DRM is 1:4. Mean current density was doubled in the cholesterol-depleted cells, without any noticeable effects on other parameters. These results demonstrate that recruitment of the K_V10.1 channel to the DRM fractions involves its functional regulation.     

Affinity partitioning of vancomycin

The use of the Flanagan and Barondes model(14) describing affinity partitioning as an aid in designing separation systems is discussed. Experimental studies are described for affinity partitioning of vancomycin, a glycopeptide antibiotic, in a water-methoxypolyethylene glycol-dextran system using methoxypolyethylene glycol-dextran system using methoxypolyethylene glycol bound D-alanyl-Dalanyl-D-alanine or D-alanyl-D-alanine as the reversible affinity ligand. Even for this ideal case of 1:1 binding interaction, the model only qualitatively predicts the affinity effect when all model parameters are measured independently. The discrepancy between measured and predicted values can be attributed to a difference in exposed surface of the free antibiotic and ligand compared to that in the bound state.The effect of experimentally varying model parameters is also described. It was determined that a polymers-ligand which partitions more strongly to the top phase would provide the most significant enhancement to this affinity partitioning system. Such an improvement can be made by increasing the molecular weight of the hydrophobicity of the polymer-ligand. A process for vancomycin recovery from fermentation broth using D--alanyl-D-alanine sepharose as affinity ligand is described.     

Cyclic electron flow and light partitioning between the two photosystems in leaves of plants with different functional types

Photosynthesis Research - Mechanisms involving ammonium toxicity, excess light, and photosynthesis are scarcely known in plants. We tested the hypothesis that high NH4+ supply in presence of high...     

Ionic partitioning and stomatal regulation: Dissecting functional elements of the genotypic basis of salt stress adaptation in grafted melon

Vegetable grafting is commonly claimed to improve crop’s tolerance to biotic and abiotic stresses, including salinity. Although the use of inter-specific graftings is relatively common, whether the improved salt tolerance should be attributed to the genotypic background rather than the grafting per se is a matter of discussion among scientists. It is clear that most of published research has to date overlooked the issue, with the mutual presence of self-grafted and non-grafted controls resulting to be quite rare within experimental evidences. It was recently demonstrated that the genotype of the rootstock and grafting per se are responsible respectively for the differential ion accumulation and partitioning as well as to the stomatal adaptation to the stress. The present paper contributes to the ongoing discussion with further data on the differences associated to salinity response in a range of grafted melon combinations.     

Control analysis of photosynthate partitioning

Experiments were carried out to investigate the contribution of ADP-glucose pyrophosphorylase and the plastid phosphoglucosemutase to the control of starch synthesis. Mutants ofArabidopsis thaliana (L.) Heyhn. were constructed with 50% and 7% of the wild-type adenosine 5′-diphosphoglucose pyrophosphorylase (ADPGlc-PPase), or 50% and null plastid phosphoglucomutase (PGM). The changes in the steady-state rates of sucrose synthesis, starch synthesis and CO₂ fixation were measured in saturating CO₂ in low (75 μmol·m⁻²·s⁻¹) and high (600 μmol·m⁻²·s⁻¹) irradiance. In low irradiance, a 50% decrease of PGM had no significant effect on fluxes, while a 50% and 93% decrease of ADPGlc-PPase led to a 23% and 74% inhibition of starch synthesis. Decreased ADPGlc-PPase led to an increase of hexose phosphates, triose phosphates and fructose-1,6-bisphosphate. Fixation of CO₂ was not inhibited because the inhibition of starch synthesis was matched by a stimulation of sucrose synthesis. In high irradiance, a 50% decrease of PGM led to a 20% inhibition of starch synthesis. A 50% and 93% decrease of ADPGlc-PPase led to a 39% and 90% inhibition of starch synthesis. Sucrose synthesis was also inhibited, and the rate of photosynthesis was decreased. Decreased ADPGlc-PPase led to an increase of hexose phosphates but triose phosphates and fructose-1,6-bisphosphate did not increase. These results are used to estimate flux-control coefficients for these enzymes for starch synthesis. Firstly, the flux to starch is only controlled by ADPGlc-PPase in low irradiance, but control is redistributed to other enzymes in the pathway when a rapid flux is imposed, e.g. in high irradiance and CO₂. Secondly, reducing the rate of starch synthesis by decreasing the activity of enzymes in this pathway does not always lead to a compensating increase in the rate of sucrose synthesis. Thirdly, decreasing the activity of an enzyme by a factor of two compared to the remainder of the pathway often leads to it exerting very considerable control. Fourthly, each enzyme starts to exert considerable control when only a fraction of its V_max activity is being utilised in vivo, for example the maximum flux at ADPGlc-PPase never exceeded 20% of the V_max activity. The summation theory is also applied to check whether additional major control sites are required. In low irradiance, the efficiency of light harvesting will exert considerable control over the rate of starch synthesis.     

Evaluating thermal resource partitioning

Summary The field thermal biology of sympatric Anolis cooki and A. cristatellus were evaluated in January and in August in desert scrub forest at Playa de Tamarindo near Guanica, Puerto Rico. Data on randomly positioned copper models of lizards, each equipped with a built-in thermocouple, established null hypotheses about basking frequency and operative temperatures (T _e) against which the behavior and body temperatures (T _b) of live lizards were evaluated. Both species exhibited non-random hourly basking rates (more marked in cristatellus than in cooki), and cristatellus was virtually inactive during the warm mid-day hours. The relationship between lizards' T _b and randomly sampled T _e differed between the species: cristatellus's mean T _b was 2° to 3° C lower than randomly sampled mean T _e in both months, whereas cooki's mean T _b was slightly higher than mean T _e in January and slightly lower in August. Although cooki's mean T _b was higher than that of cristatellus in both months, the T _b's of the two species overlapped substantially over an annual cycle. Given the similarities in their field active T _b and the low thermal heterogeneity among microsites at Playa de Tamarindo, these species appear not to partition the thermal environment there in a coarse-grained way. Instead, the relatively small differences in their field active T _b probably result from small differences in their use of similar microhabitats within their mutually exclusive territories. Thermal resource partitioning by territorial animals is unlikely unless thermal heterogeneity is coarse-grained in relation to territory size.