Multi-compartmental modelling and experimental design for glucose transport studies in insulin-resistant rats

Many pathologies are associated with abnormalities of glucose metabolism or with perturbations of its transport (type 2 diabetes or insulin-resistance). The pre-diabetic state is characterised by a state of insulin-resistance, in others words a defect of glucose transport in insulin-sensible tissues, such as muscles and adipose tissues. The mathematical modelling of experimental data can be an excellent method to explore the mechanisms implied in the studied biological phenomenon. Thus, starting from a symbolic formulation like the compartmental modelling, it can be possible to develop a theoretical basis for the observation and to consider the best-adapted experiments for the study. We showed with mathematical models that [123I]-6-deoxy-6-iodo-D-glucose (6-DIG), shown as a tracer of glucose transport in vitro, could point out this transport abnormality. To quantify the insulin resistance, we estimated the fractional transfer coefficients of 6-DIG from the blood to the organs. We realised many studies to lead to a satisfying model; special attention has been paid to the precision of the parameter to select the best model. The results showed that by associating experimental data obtained with 6-DIG activities and an adapted mathematical model, discriminating parameters (in and out fractional transfer coefficients) between the two groups (control and insulin-resistant rats) could be pointed out.     

Estimation of Frankia growth using Bradford protein and INT reduction activity estimations: application to inoculum standardization

Abstract The growth of Frankia spp. strain ORS 020607 in BAP medium was studied by using two methods simultaneously: determination of Bradford protein content and INT (2-( p -iodophenyl-3-( p -nitrophenyl)-5-phenyl tetrazolium chloride ) reduction activity (IRA). With the latter test, red formazan crystals formed intracellularly were extracted with methanol. Colouration intensity was estimated by absorbance spectrophotometry at 490 nm. The protein content and IRA of the culture were monitored for 96 days. IRA appeared to reflect the 'metabolically active' biomass of Frankia more accurately than the Bradford protein estimations.     

Phylogenetic mixture models for proteins

Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors: genetic code; solvent exposure; secondary and tertiary structure; protein function; etc. These impact the substitution pattern and, in most cases, a single replacement matrix is not enough to represent all the complexity of the evolutionary processes. This paper explores in maximum-likelihood framework phylogenetic mixture models that combine several amino acid replacement matrices to better fit protein evolution.We learn these mixture models from a large alignment database extracted from HSSP, and test the performance using independent alignments from TREEBASE.We compare unsupervised learning approaches, where the site categories are unknown, to supervised ones, where in estimations we use the known category of each site, based on its exposure or its secondary structure. All our models are combined with gamma-distributed rates across sites. Results show that highly significant likelihood gains are obtained when using mixture models compared with the best available single replacement matrices. Mixtures of matrices also improve over mixtures of profiles in the manner of the CAT model. The unsupervised approach tends to be better than the supervised one, but it appears difficult to implement and highly sensitive to the starting values of the parameters, meaning that the supervised approach is still of interest for initialization and model comparison. Using an unsupervised model involving three matrices, the average AIC gain per site with TREEBASE test alignments is 0.31, 0.49 and 0.61 compared with LG (named after Le & Gascuel 2008 Mol. Biol. Evol. 25, 1307-1320), WAG and JTT, respectively. This three-matrix model is significantly better than LG for 34 alignments (among 57), and significantly worse for 1 alignment only. Moreover, tree topologies inferred with our mixture models frequently differ from those obtained with single matrices, indicating that using these mixtures impacts not only the likelihood value but also the output tree. All our models and a PhyML implementation are available from http://atgc.lirmm.fr/mixtures.     

Species richness declines and biotic homogenisation have slowed down for NW‐European pollinators and plants

Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20‐year periods, comparing periods of rapid land‐use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post‐1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large‐scale land‐use intensification and natural habitat loss has ceased.     

Abundance and distribution of endangered Franciscana dolphins in Argentine waters and conservation implications

This is the first study in Argentine waters on the abundance of the threatened Franciscana dolphin, Pontoporia blainvillei . During 2003–2004 we carried out 17 aerial surveys using line transect sampling methodology. We observed 101 Franciscanas in 71 sightings. In northern areas density was estimated at 0.106 individual/km². Density was lower in southern areas (0.055/km²) and declined with depth beyond 30-m isobaths (0.05/km²). A correction factor for submerged dolphins was applied to density and then extrapolated to the strip between the coastline and the 30-m isobath. Abundance in the northern area was estimated at 8,279 (4,904–13,960) individuals, while in the southern area it was estimated at 5,896 (1,928–17,999) individuals. Considering an annual mortality of about 500–800 individuals, about 3.5%–5.6% of the stock may be removed each year by the fishery and over the 2% recommended by the International Whaling Commission (IWC) and may not be sustainable by the population. Higher densities in coastal areas make Franciscanas more vulnerable to coastal fishing camps, which increased mortality in recent years. A remarkable finding was that while density decreases to the south, values of catch per unit effort (CPUE) increases, indicating different catchability of dolphins between areas.     

Population size estimates based on the frequency of genetically assigned parent–offspring pairs within a subsample

Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent–offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent–offspring pairs can be determined. The study's aim was to clarify whether a classical capture–mark–recapture (CMR) method can be adapted or extended by this genetic element to a genetic‐based capture–mark–recapture (g‐CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R‐code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one‐time subsample. This is especially of value where traditional CMR methods or other DNA‐based (fecal or hair) capture–recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g‐CMR method is ecologically and hunting‐wise appropriate, it enables a wide applicability, also through its species‐independent use.     

Assessing the ecological stress in a Garonne River stretch,southwest France

In order to assess the level of ecological stress caused by the pollution from local disturbances in a stretch of the Garonne River, France, we applied the Abundance-Biomass Comparison (ABC) index, using fish assemblages. Data were collected in a 10-year span (1992–2002) in a reference site and in two pollution-exposed sites. The ABC index mean value in the reference site (S1) was 0.03 ± 0.002 (95% Confidence Interval – CI); for the polluted sites (S2 and S3), the values were −0.09 ± 0.002 (95% CI) and −0.12 ± 0.002 (95% CI), respectively. The ABC index showed that, besides flow variations, both downstream sites are statistically different (p < 0.05) from the reference site, but all three seem to be under moderate stress. Furthermore, we related our ABC scores to water quality and flow regime variables in the reference site and one of the polluted sites by means of a cluster analysis. The results showed that, in the reference site, the ABC scores are closely related to the flow regime, while in the polluted site, downstream a urban area, ABC is related to water quality variables such as phosphates and total phosphorous. We argue that ecological indicators can help decisions on environmental damage liability.     

Species richness estimations of the megadiverse scuttle fly genus Megaselia (Diptera: Phoridae) in a wildfire‐affected hemiboreal forest

Abstract The species richness of the scuttle fly (Diptera: Phoridae) genus Megaselia was estimated by various non‐parametric estimators from EstimateS, Species Prediction And Diversity Estimation (SPADE) and Ws2m, based on material from a Swedish hemiboreal forest area recently affected by major wildfires, Tyresta National Park and Nature Reserve (TNPNR), south of Stockholm. A total of 21 249 individuals were collected in Malaise traps, of which males constituted 16 976 and females 4 273. The analysed dataset represents 37 samples containing 18 549 specimens sorted into 330 species (184 described, 146 are either undescribed or of unsettled taxonomic status). It was not possible to estimate the total species richness using all samples due to heterogeneity caused by inclusion of different communities and temporal incoherencies between samples within and between years. Even with material obtained from a sampling program that was not designed for species richness estimates, it was possible to obtain reliable results when sample heterogeneity was minimized. By dividing the data into community‐specific datasets – for bog, forest and wildfire – it was possible to obtain asymptotic curves for the smaller of the two wildfire datasets. A total estimate of 357–439 (95% CI) was attained by using the smaller wildfire dataset and adding the 85 unique species from the samples not included in the estimation analysis. TNPNR has one of the richest known scuttle fly communities in Europe, consisting of almost 50% of the currently named Megaselia species; 48 of these species are reported as new records for Sweden in this study.     

Inventorying the fungi of Mexico

Conservation of the vegetation, analysis of the knowledge of the diversity of fungi, new biological methods and estimates of the numbers of species of fungi that grow in Mexico are discussed. The great forest destruction that is occurring and the loss of fungal diversity in the country is seriously depleting total biodiversity, mainly in the tropics. Methods to establish the number of Mexican species of fungi are proposed based on an average of: (1) the numbers of fungal obligates of vascular plants and animals and of the saprobic species; (2) extrapolating the number of the British fungi to Mexico, taking the British mycota as the best known in the world; and (3) extrapolating to the country the number of species known to occur in the State of Veracruz (Mexico), the best known in the country. The average of these three calculations yields about 200 000 species of fungi for Mexico. Of these, only 3.5% are known, despite considerable progress having been made in the inventory of the country's fungi in the last 30 years. It is concluded that it is necessary to place more emphasis on alpha taxonomy, to train more specialists and to prepare monographs of several groups of fungi.