Microsomal and cytosolic cytochrome P450 mediated benzo(a)pyrene hydroxylation in Pleurotus pulmonarius

Summary Microsomal and soluble fractions of Pleurotus pulmonarius exhibited a reduced carbon monoxide difference spectrum with P450 maxima at 448nm and 450–452nm respectively. Substrate induced Type I spectra were observed on addition of benzo(a)pyrene to both fractions. Benzo(a)pyrene hydroxylation was measured using the aryl hydrocarbon hydroxylase assay and was observed to be P450 dependent as indicated by carbon monoxide inhibition together with the substrate binding characteristics. The activity of the fractions were observed to give K_m of 200mM and 660mM and V_max of 1.25 nmol/min/nmol P450 and 0.57 nmol/min/nmol P450 for the microsomal and cytosolic fractions respectively.     

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.     

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

Increased energy promotes size-based niche availability in marine mollusks

Variation in chemical energy, that is food availability, is posited to cause variation in body size. However, examinations of the relationship are rare and primarily limited to amniotes and zooplankton. Moreover, the relationship between body size and chemical energy may be impacted by phylogenetic history, clade-specific ecology, and heterogeneity of chemical energy in space and time. Considerable work remains to both document patterns in body size over gradients in food availability and understanding the processes potentially generating them. Here, we examine the functional relationship between body size and chemical energy availability over a broad assortment of marine mollusks varying in habitat and mobility. We demonstrate that chemical energy availability is likely driving body size patterns across habitats. We find that lower food availability decreases size-based niche availability by setting hard constraints on maximum size and potentially on minimum size depending on clade-specific ecology. Conversely, higher food availability promotes greater niche availability and potentially promotes evolutionary innovation with regard to size. We posit based on these findings and previous work that increases in chemical energy are important to the diversification of Metazoans through size-mediated niche processes.     

Changes in upland bird abundances show associations with moorland management

Capsule: Changes in abundance of six bird species showed associations with moorland management.

Aims: To assess responses of breeding birds to moorland management over a 14-year period.

Methods: Vegetation and birds were surveyed at 2–3-year intervals and changes examined in relation to sheep and cattle grazing, vegetation burning and cutting.

Results: Seven correlations between change in management and change in bird abundance were detected, and six between change in vegetation and change in bird abundance. On plots where sheep numbers declined, Golden Plover Pluvialis apricaria and Northern Wheatear Oenanthe oenanthe declined. Where a greater area was burned, Golden Plover increased in the initial post-burning period but Red Grouse Lagopus lagopus scotica declined. Eurasian Curlew Numenius arquata and Sky Lark Alauda arvensis increased where a greater area of moorland vegetation was cut. Whinchat Saxicola rubetra declined with increasing cattle numbers on a plot.

Conclusions: Bird populations respond to changes in moorland management, but these changes are not always associated with detectable changes in vegetation. These responses of moorland breeding birds to management could help refine agri-environment options and other conservation interventions on moorland. Responses differed between bird species, ideally requiring site-specific planning where managing for multiple species is a goal.     

Climate change and annual survival in a temperate passerine: partitioning seasonal effects and predicting future patterns

Predicting climate change impacts on population size requires detailed understanding of how climate influences key demographic rates, such as survival. This knowledge is frequently unavailable, even in well‐studied taxa such as birds. In temperate regions, most research into climatic effects on annual survival in resident passerines has focussed on winter temperature. Few studies have investigated potential precipitation effects and most assume little impact of breeding season weather. We use a 19‐year capture–mark–recapture study to provide a rare empirical analysis of how variation in temperature and precipitation throughout the entire year influences adult annual survival in a temperate passerine, the long‐tailed tit Aegithalos caudatus. We use model averaging to predict longer‐term historical survival rates, and future survival until the year 2100. Our model explains 73% of the interannual variation in survival rates. In contrast to current theory, we find a strong precipitation effect and no effect of variation in winter weather on adult annual survival, which is correlated most strongly to breeding season (spring) weather. Warm springs and autumns increase annual survival, but wet springs reduce survival and alter the form of the relationship between spring temperature and annual survival. There is little evidence for density dependence across the observed variation in population size. Using our model to estimate historical survival rates indicates that recent spring warming has led to an upward trend in survival rates, which has probably contributed to the observed long‐term increase in the UK long‐tailed tit population. Future climate change is predicted to further increase survival, under a broad range of carbon emissions scenarios and probabilistic climate change outcomes, even if precipitation increases substantially. We demonstrate the importance of considering weather over the entire annual cycle, and of considering precipitation and temperature in combination, in order to develop robust predictive models of demographic responses to climate change. Synthesis Prediction of climate change impacts demands understanding of how climate influences key demographic rates. In our 19‐year mark‐recapture study of long‐tailed tits Aegithalos caudatus, weather explained 73% of the inter‐annual variation in adult survival; warm springs and autumns increased survival, wet springs reduced survival, but winter weather had little effect. Robust predictions thus require consideration of the entire annual cycle and should not focus solely on temperature. Unexpectedly, survival appeared not to be strongly density‐dependent, so we use historical climate data to infer that recent climate change has enhanced survival over the four decades in which the UK long‐tailed tit population has more than doubled. Furthermore, survival rates in this species are predicted to further increase under a wide range of future climate scenarios.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.