Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies

Amphotericin B (AmB) is a polyene macrolide antibiotic used to treat systemic fungal infections. The molecular mechanism of AmB action is still only partly characterized. AmB interacts with cell-membrane components and forms membrane channels that eventually lead to cell death. The interaction between AmB and the membrane surface can be regarded as the first (presumably crucial) step on the way to channel formation. In this study molecular dynamics simulations were performed for an AmB–lipid bilayer model in order to characterize the molecular aspects of AmB–membrane interactions. The system studied contained a box of 200 dimyristoylphosphatidylcholine (DMPC) molecules, a single AmB molecule placed on the surface of the lipid bilayer and 8,065 water molecules. Two molecular dynamics simulations (NVT ensemble), each lasting 1 ns, were performed for the model studied. Two different programs, CHARMM and NAMD2, were used in order to test simulation conditions. The analysis of MD trajectories brought interesting information concerning interactions between polar groups of AmB and both DMPC and water molecules. Our studies show that AmB preferentially took a vertical position, perpendicular to the membrane surface, with no propensity to enter the membrane. Our finding may suggest that a single AmB molecule entering the membrane is very unlikely.Figure The figure presents the whole structure of the system simulated—starting point. AmB is presented as a space-filling model, DMPC molecules—green sticks, water molecules—red sticks     

Further evidence that oxidative stress may be a risk factor responsible for the development of atherosclerosis

There are numerous data suggesting that oxidative stress may be involved in the development of atherosclerosis. Therefore, in the present study we measured the amount of 8-hydroxy-2'-deoxyguanosine (8-OH-dG), one of the typical biomarkers of oxidative stress, in DNA isolated from lymphocytes of the patients and in the control group. Levels of antioxidant vitamins (A, C, and E) and intracellular labile iron pool (LIP), which can influence oxidative stress, were also determined. Blood samples were obtained from a control group of 55 healthy persons and from 43 atherosclerotic patients. 8-OH-dG and the vitamin levels were measured by high-performance liquid chromatography. Labile iron pool in lymphocytes was analyzed by fluorescent assay. The levels of 8-OH-dG and LIP were significantly higher and vitamin C concentration was significantly lower in the patient group than in the control group. The rest of the analyzed parameters do not significantly differ between the groups. A lower concentration of vitamin C and higher levels of labile iron pool in a group of atherosclerotic patients when compared with the control group may lead to oxidative stress, which is manifested by a higher level of 8-OH-dG in blood lymphocytes. All these factors may create an environment that promotes the development of atherosclerosis.     

Winter severity limits red fox populations in Eurasia

Aim  We investigated geographical variation in the density of the red fox in relation to climatic variables, habitat productivity and seasonality to identify those factors that were the best predictors of fox density.
Location  Published data on red fox abundance were collated from 69 locations over Europe and Asia.
Methods  Using generalized linear models and the information-theoretic approach, we analysed the contribution of climatic measures (winter and summer temperature, mean snow depth and duration), primary productivity and seasonality indices [based on the fraction of photosynthetically active radiation (FPAR) index] to account for variation in red fox density.
Results  Red fox density in winter ranged from 0.001–2.8 individuals km⁻²; the average density was 0.21 individuals km⁻². Variation in red fox density was best explained by the winter temperature and seasonality. Density decreased with declining winter and summer temperatures, increasing degree of seasonality and increasing duration of snow cover. There was no relationship with habitat productivity.
Main conclusions  Our results indicate that winter climatic conditions and seasonality, but not habitat productivity, may limit red fox density in Eurasia. One explanation for the limitation of the red fox population may be the fox's physiological capability to cope with abiotic conditions. Concurrently, the severity of winter may lead to reduced availability of the fox's prey. That, together with a shorter reproductive period may result in lower reproductive output as well as lower survival of adults and cubs.     

Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species <Emphasis Type="Italic">Solanum verrucosum</Emphasis> through DNA capture technologies

Key message

A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes.

Abstract

We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62–56.98 Mb.

     

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.     

Climate change as a possible driver of invasion and differential in HSP70 expression in two genetically distinct populations of the invasive killer shrimp, <Emphasis Type="Italic">Dikerogammarus villosus</Emphasis>

Global climate change is known to affect physiological processes in charge of cellular stress response. That often results in forcing many organisms to shift their biogeographic distribution ranges. It also holds true for euryoecious and highly invasive species like the killer shrimp, Dikerogammarus villosus. In this study we compare the level of response to thermal stress in two genetically diversified populations of the amphipod D. villosus on the cellular level, namely HSP70 expression. The results show clear difference in HSP70 expression, that can be a direct consequence of the different climatic conditions both populations faced along their invasion routes. We conclude that the eastern population of D. villosus is more sensitive to thermal stress than the western population, hence its invasion potential may be lower than that of the latter. Considering the thermal tolerance of both populations and global warming, we can make some predictions about further spread of D. villosus, including the possibility of an emergence of the super-invader that may arise after cross-breeding of both populations, imposing even larger threat to the freshwater ecosystems.     

The seeds of success: release from fungal attack on seeds may influence the invasiveness of alien <Emphasis Type="Italic">Impatiens</Emphasis>

Although closely related, Impatiens glandulifera and Impatiens balfourii differ in their invasiveness in Europe; only the former is highly invasive there. Following the assumptions of the enemy release hypothesis (ERH), we tested whether these differences may be explained by the levels of seed infestation by pathogenic fungi. Using seeds collected along the Swiss-Italian border, we recorded four true pathogens of seeds: Fusarium culmorum, F. oxysporum, F. sporotrichoides, and Giberella avenacea. In Italy the seeds of I. balfourii were infected by fungal pathogens more often than those of I. glandulifera, while in Switzerland both species were under the same level of pressure. However, the overall differences in pathogen abundance were consistent with the ERH: seeds of the more invasive species were attacked less. This could be a result of differences between the communities of fungal pathogens attacking the seeds of both species in each country. The number of colonies of secondary pathogens (Cladosporium cladosporioides, Alternaria alternata) correlated negatively with the number of colonies of true pathogens; we suggest that the secondary pathogens may have prevented the occurrence of the true pathogens. The reason for the between-country differences in the fungal pathogen communities is unclear. A possible explanation is that Italy and Switzerland differ in their road and green-area maintenance work schemes, which may have influenced pathogen pressure on seeds. This study is one of the few that offers results indicating that release from enemies may be crucial to the invasion success of plants as early as the seed stage.     

MHC influences infection with parasites and winter survival in the root vole Microtus oeconomus

Selective pressure from parasites is thought to maintain the polymorphism of major histocompatibility complex (MHC) genes. Although a number of studies have shown a relationship between the MHC and parasitic infections, the fitness consequences of such associations are less well documented. In the present paper, we characterised the variation in exon 2 of MHC class II DRB gene in the root vole and examined the effects of that gene on parasite prevalence and winter survival. We identified 18 unique exon 2 sequences, which translated into 10 unique amino acid sequences. Phylogenetic analysis revealed the presence of three distinct clusters, and allele distributions among these individuals suggested that the clusters correspond to three different loci. Although the rate of synonymous substitutions (d_S) exceeded the rate of nonsynonymous substitutions (d_N) across sequences, implying purifying selection, d_N was significantly elevated at antigen-binding sites, suggesting that these sites could be under positive selection. Screening for parasites revealed a moderate prevalence of infection with gastrointestinal parasites (24 % infected), but a high infection rate for blood parasites (56 % infected). Infection with the blood parasite Babesia ssp. decreased survival almost twofold (25.7 vs. 13.9 %). Animals possessing the amino acid sequence AA*08 survived better than others (44.9 vs. 22 %), and they were infected with Babesia ssp. less often (13.9 vs 25.7 %). In contrast, individuals carrying allele AA*05 were infected more often (31.7 vs. 15.3 %). Heterozygosity at one of the putative loci was associated with a lower probability of infection with Babesia ssp., but at the other locus, the association was reversed. The unexpected latter result could be at least partly explained by the increased frequency of the susceptible allele AA*05 among heterozygotes. Overall, we demonstrate that infection with Babesia ssp. is a strong predictor of winter survival and that MHC genes are important predictors of infection status as well as survival in the root vole.     

A comparison of the therapeutic and reactivating efficacy of newly developed bispyridinium compounds (K206, K269) with currently available oximes against tabun in rats and mice

The potency of newly developed bispyridinium compounds (K206, K269) in reactivating tabun-inhibited acetylcholinesterase and eliminating tabun-induced lethal toxic effects was compared with commonly used oximes (obidoxime, trimedoxime, the oxime HI-6) using in vivo methods. Studies which determined percentage of reactivation of tabun-inhibited blood and tissue AChE in poisoned rats showed that the reactivating efficacy of both newly developed oximes is comparable with obidoxime and trimedoxime in blood but lower than the reactivating potency of trimedoxime and obidoxime in the diaphragm and brain. Nevertheless, the differences in reactivating efficacy of obidoxime, trimedoxime and K206 was not significant while the potency of K269 to reactivate tabun-inhibited acetylcholinesterase was significantly lower. Both newly developed oximes were also found to be relatively efficacious in elimination of the lethal toxic effects in tabun-poisoned mice. Their therapeutic efficacy corresponds to the therapeutic potency of obidoxime. The oxime HI-6, relatively efficacious against soman, did not seem to be an adequately effective oxime in reactivation of tabun-inhibited AChE and to counteract lethal effects of tabun. Both newly developed oximes (K206, K269) are significantly more efficacious in reactivating tabun-inhibited AChE in rats and to eliminate lethal toxic effects of tabun in mice than the oxime HI-6 but their reactivating and therapeutic potency does not prevail over the effectiveness of currently available obidoxime and trimedoxime and, therefore, they are not suitable for their replacement of commonly used oximes for the treatment of acute tabun poisoning.