Evaluation of residue variability in a conformation‐specific context and during evolutionary sequence reconstruction narrows drug resistance selection in Abl1 tyrosine kinase

Diseases with readily available therapies may eventually prevail against the specific treatment by the acquisition of resistance. The constitutively active Abl1 tyrosine kinase known to cause chronic myeloid leukemia is an example, where patients may experience relapse after small inhibitor drug treatment. Mutations in the Abl1 tyrosine kinase domain (Abl1‐KD) are a critical source of resistance and their emergence depends on the conformational states that have been observed experimentally: the inactive state, the active state, and the intermediate inactive state that resembles Src kinase. Understanding how resistant positions and amino acid identities are determined by selection pressure during drug treatment is necessary to improve future drug development or treatment decisions. We carry out in silico site‐saturation mutagenesis over the Abl1‐KD structure in a conformational context to evaluate the in situ and conformational stability energy upon mutation. Out of the 11 studied resistant positions, we determined that 7 of the resistant mutations favored the active conformation of Abl1‐KD with respect to the inactive state. When, instead, the sequence optimization was modeled simultaneously at resistant positions, we recovered five known resistant mutations in the active conformation. These results suggested that the Abl1 resistance mechanism targeted substitutions that favored the active conformation. Further sequence variability, explored by ancestral reconstruction in Abl1‐KD, showed that neutral genetic drift, with respect to amino acid variability, was specifically diminished in the resistant positions. Since resistant mutations are susceptible to chance with a certain probability of fixation, combining methodologies outlined here may narrow and limit the available sequence space for resistance to emerge, resulting in more robust therapeutic treatments over time.     

First evidence of genotypes Ad3a16 and Ad3a18 in North America, obtained by genetic analysis of infectious human adenovirus from wastewaters of two urban communities in Canada

A 1-year study found seven infectious human adenovirus serotypes, including Ad3, Ad31, Ad46, Ad27, Ad22, Ad51, and clinical clone PB3, in wastewaters of two major cities in Canada. Comparative genomic analysis revealed the existence of the reportedly highly contagious Ad3a16/18 genotypes. This is the first report of Ad3a16/18 genotypes in North America.     

Production of biomass, carotenoid and other lipid metabolites by several red yeast strains cultivated on waste glycerol from biofuel production – a comparative screening study

This study was focused on a comparison of growth and production properties of seven red yeast strains of the genus Rhodotorula, Sporobolomyces and Cystofilobasidium cultivated on glycerol substrate. Production of enriched yeast biomas and specific yeast metabolites (carotenoids, ergosterol, lipids) was evaluated on medium with glucose, pure technical glycerol and/or waste glycerol from biofuel production (40 g/L) and mixture of glycerol and glucose (1:3, 1:1, 3:1; C/N ratio 57 in all cultivations). All tested strains were able to utilize glycerol as the only carbon source. Production of biomass on waste glycerol was in most strains higher than in control as well as in medium with pure technical glycerol and reached 15.97–21.76 g/L. Production of carotenoids and ergosterol was better in glucose medium than in medium with glycerol only. Nevertheless, using glycerol medium with addition of glucose, higher yields of total carotenoids, beta-carotene and ergosterol were obtained than in control. The highest yields of total pigments were reached by Sporobolomyces roseus (3.60 mg/g cell dry weight (CDW); glycerol:glucose 1:3), Sporobolomyces salmonicolor (2.85 mg/g CDW; glycerol:glucose 1:3) and Rhodotorula glutinis (2.80 mg/g CDW; glycerol:glucose 3:1) In glucose medium, most tested strains except Cystofilobasidium capitatum (22.6 %) produced neutral lipids in the range of 11–15 %. Production of triacylglycerols in all strains was in 10–30 % better in glycerol medium, in which Rhodotorula aurantiaca and Sporobolomyces shibatanus also reached intracellular triacylglycerol concentrations up to 20 % of biomass. This study has shown that oleaginous red yeasts could have great potential for converting crude glycerol to valuable lipids and carotenoids in respect of efficient bioresources utilization.     

The Effects of Stabilizing and Directional Selection on Phenotypic and Genotypic Variation in a Population of RNA Enzymes

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population’s response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.     

Estimation of Linkage and Association from Allele Transmission Data

The TDT provides a hypothesis test for the presence of linkage or association (linkage disequilibrium). However, since the TDT is a single test statistic, it cannot be used to separate association and linkage. The importance of this difficulty, following a significant TDT result, has been recently emphasized by Whittaker , Denham and Morris (2000), who alert the community to the possibility that a significant TDT may result from loose linkage and strong association, or from tight linkage and weak association. To attack this problem we start with the parametric model for family‐based allele transmission data of Sham and Curtis (1995) (or Sham (1998)) and find that the parameters in the model are not always identifiable. So we introduce a reparameterization that resolves the identifiability issues and leads to a valid likelihood ratio (LR) test for linkage. Since the linkage and association parameters are both of interest, we next introduce and apply an integrated likelihood (IL) approach to provide separate point estimates and confidence intervals for these parameters. The estimates are shown to have generally small bias and mean square error, while the confidence intervals have good average length and coverage probabilities. We compare the power of the IL approach for testing linkage and, separately association, with the TDT and LR.     

Seasonal distribution of pollen in the atmosphere of Darwin,tropical Australia: Preliminary results

Pollen loads in the atmosphere of Darwin, a city located in the wet‐dry tropics of Australia, have been monitored for the period March 2004 to November 2005 as part of a large research program looking at atmospheric particles and human health. Seven pollen types dominate the pollen spectrum, the herbaceous families of Poaceae (grasses) and Cyperaceae (sedges), as well as several native tree and shrub taxa, Acacia, Callitris, Casuarina, Arecaceae and Myrtaceae. The pollen loads were found to have a strong seasonal component associated with the alternating wet (November to March) and dry (April to October) seasons of the region. Seventy percent of the yearly pollen load is captured during the dry season, with the peak pollen period occurring at the onset of the dry season (April–May) when most grasses are in flower. The daily pollen concentration decreases as the dry season progresses, accompanied by a change in composition; fewer herbaceous but increasing woody taxa. Preliminary health outcomes reveal a positive association between hay fever, Poaceae and Acacia pollen, as well as a significant association between total fungal spore concentrations and asthma. The Darwin record contrasts significantly with surveys conducted in the subtropical and temperate cities of Australia where temperature as opposed to rainfall and the prevalence of northern hemisphere exotic tree species have a greater influence over the seasonality and composition of the pollen loads.     

Late quaternary vegetation dynamics and human impact on Alexander Selkirk Island, Chile

Aim To reconstruct the history of vegetation and environments using pollen, charcoal and sediment analysis, and to identify the timing and nature of climate change and human impact on the vegetation of a remote Pacific island. Location Cerro de Los Inocentes, 1000 m above sea level, Alexander Selkirk Island (33°45′S, 80°45′W), Chile. The westernmost island of the Juan Fernandez Archipelago, south‐east Pacific Ocean. Methods A 150‐cm long sediment core comprising 87 cm dark brown peat overlying 63 cm of yellow grey clay was extracted from a shallow depression on the southern slopes of Cerro de Los Inocentes. Pollen, charcoal, sediment and accelerator mass spectrometry radiocarbon analyses were used to construct a record of vegetation change through time. Numerical analysis of multispecies data allowed the classification of fossil assemblages into distinct pollen zones. Results Pollen and spores are preserved throughout the sediment with high concentrations coinciding with the beginning of organic sediment accumulation at around 8000 ¹⁴C yr BP. Prior to 8000 ¹⁴C yr BP, the deposition of clays, presumably from upslope erosion, occurred in a landscape sparsely vegetated by grasses, ferns and Pernettya rigida heath, including several plants that are only found 100–200 m above the site today (Zone CI‐1). After 8000 ¹⁴C yr BP, a P. rigida heath was the dominant vegetation (Zone CI‐2). A shift to a wet heath–shrubland (Zone CI‐3) occurred at 6000 ¹⁴C yr BP and was followed by a transition to a treefern–shrubland mosaic accompanied by periodic burning (Zone CI‐4) after 4500 ¹⁴C yr BP. The impact of human occupation is evident in Zone CI‐5 at 450 ¹⁴C yr BP with the loss of forest species, increased burning and invasion of the exotic plant Rumex. Main conclusions The pollen and charcoal record provides the first evidence of vegetation changes spanning at least the last 8000 ¹⁴C yr BP from the high altitude environment of Alexander Selkirk Island. Prior to 8000 ¹⁴C yr BP, the altitudinal ranges of different plant species may have been suppressed by a cooler and drier climate. Increasing precipitation and temperatures at the end of the last glacial period may have mobilized exposed sediments in a sparsely vegetated upland environment, altering local drainage patterns, eventually leading to slope stabilization and deposition of organic detritus under an increasing density of heath and shrub vegetation. The subalpine heath–shrubland persisted until 4500 ¹⁴C yr BP when first evidence for sustained burning is found in association with the establishment of a more open treefern–shrubland vegetation pattern. In the absence of human occupation at this time, the influence of increased climatic variability associated with more frequent El Niño‐Southern Oscillation events during the mid to late Holocene is considered one of the main driving forces behind increased vegetation disturbance during this period. The record provides evidence that island vegetation patterns have been highly dynamic over millennial to decadal time‐scales and that the flora has persisted through periods of rapid and major climate change. This changed with the discovery of the island by European explorers in the late sixteenth century and the subsequent introduction of goats and exploitation and burning of forests, which resulted in the progressive destruction of native vegetation and the invasion of introduced plants. There is evidence that reduced burning and control of the goat population within the last 50 years has resulted in marginal recovery of some high altitude native plant species.     

Architectural and thermodynamic principles underlying intramembrane protease function

Intramembrane proteases hydrolyze peptide bonds within the membrane as a signaling paradigm universal to all life forms and with implications in disease. Deciphering the architectural strategies supporting intramembrane proteolysis is an essential but unattained goal. We integrated new, quantitative and high-throughput thermal light-scattering technology, reversible equilibrium unfolding and refolding and quantitative protease assays to interrogate rhomboid architecture with 151 purified variants. Rhomboid proteases maintain low intrinsic thermodynamic stability (ΔG = 2.1-4.5 kcal mol(-1)) resulting from a multitude of generally weak transmembrane packing interactions, making them highly responsive to their environment. Stability is consolidated by two buried glycines and several packing leucines, with a few multifaceted hydrogen bonds strategically deployed to two peripheral regions. Opposite these regions lie transmembrane segment 5 and connected loops that are notably exempt of structural responsibility, suggesting intramembrane proteolysis involves considerable but localized protein dynamics. Our analyses provide a comprehensive 'heat map' of the physiochemical anatomy underlying membrane-immersed enzyme function at, what is to our knowledge, unprecedented resolution.