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.     

The role of test accuracy in predicting acceptance of genetic susceptibility testing for Alzheimer's disease

A survey questionnaire regarding perceptions of risk and genetic susceptibility to Alzheimer's disease (AD) was completed by 518 offspring of AD cases from families with multiple affected, ascertained as part of a genetic linkage study of late onset AD. The questionnaire focused on respondents' perceptions of their own risk for AD as well as on the properties of real and hypothetical susceptibility tests, including error rates for false-positive and false-negative test results. Our findings showed that about 20% of the sample would refuse a susceptibility test with zero error rates, about 40% would accept tests with very high error rates in both directions, and the remainder would exercise some discrimination. Acceptance of high test error rates was significantly associated with male gender, low education, and high perceived lifetime risk of AD. In a previous paper related to this work, we showed that physicians caring for these families exercised much more discrimination in judging the acceptability of genetic tests they would offer to these same respondents. The findings show that there is a pressing need to educate the public, particularly those with relatives affected by a complex disease, to expect standards of accuracy for genetic tests comparable to those that prevail in other diagnostic and prognostic testing efforts in the broad field of clinical medicine.     

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.     

Population and clonal level responses of a perennial grass following fire in the northern Chihuahuan Desert

Relationships involving fire and perennial grasses are controversial in Chihuahuan Desert grasslands of southern New Mexico, USA. Research suggests that fire delays the resprouting of perennial grasses well after two growing seasons. However, such results are confounded by livestock grazing, soil erosion, and drought. Additionally, post-fire grass responses may depend on initial clone size. We evaluated the effects of fire, grazing, and clone size on Bouteloua eriopoda (black grama) in southern New Mexico grasslands. Four 2-ha plots were established in each of four sites. Fire and grazing were applied or not applied in 1999 such that four treatment combinations were assigned randomly to plots within each site. Within each plot, small (0–10 cm² basal area), medium (10–30 cm²), and large ( > 30 cm²) clones were initially mapped in five 0.91-m² quadrats where grass attributes and litter cover were evaluated before and at the end of two growing seasons following fire. Maximum fire temperature was also measured. At a population level, canopy and litter cover were each approximately 50% less in burned than unburned areas. However, compared to initial levels, canopy height had increased by 10% at the end of the study, regardless of fire. At a clonal level, basal cover reductions were attributed mostly to large clones that survived fire. Smaller clone densities had decreased by as much as 19% in burned compared to unburned areas, and fire reduced the basal cover of medium clones. Basal and canopy cover, recruitment, and clone basal area decreased with increased fire temperatures. Almost all responses were independent of grazing, and interactive effects of grazing and fire were not detected. Fire did not kill all perennial grass clones, regardless of size. However, rapid responses were likely influenced by above-average precipitation after fire. Future studies in desert grasslands should examine how perennial grass dynamics are affected by fire, precipitation patterns, and interactions with grazing.     

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.     

Adverse effects of tempol on hidrosaline balance in rats with acute sodium overload

We studied the effects of tempol, an oxygen radical scavenger, on hydrosaline balance in rats with acute sodium overload. Male rats with free access to water were injected with isotonic (control group) or hypertonic saline solution (0.80 mol/l NaCl) either alone (Na group) or with tempol (Na-T group). Hydrosaline balance was determined during a 90 min experimental period. Protein expressions of aquaporin 1 (AQP1), aquaporin 2 (AQP2), angiotensin II (Ang II) and endothelial nitric oxide synthase (eNOS) were measured in renal tissue. Water intake, creatinine clearance, diuresis and natriuresis increased in the Na group. Under conditions of sodium overload, tempol increased plasma sodium and protein levels and increased diuresis, natriuresis and sodium excretion. Tempol also decreased water intake without affecting creatinine clearance. AQP1 and eNOS were increased and Ang II decreased in the renal cortex of the Na group, whereas AQP2 was increased in the renal medulla. Nonglycosylated AQP1 and eNOS were increased further in the renal cortex of the Na-T group, whereas AQP2 was decreased in the renal medulla and was localized mainly in the cell membrane. Moreover, p47-phox immunostaining was increased in the hypothalamus of Na group, and this increase was prevented by tempol. Our findings suggest that tempol causes hypernatremia after acute sodium overload by inhibiting the thirst mechanism and facilitating diuresis, despite increasing renal eNOS expression and natriuresis.     

Creosotebush vegetation after 50 years of lagomorph exclusion

In 1939, an experiment was established on the Jornada Experimental Range to evaluate the effects of shrub removal, rabbit exclusion, furrowing, and seeding in creosotebush [Larrea tridentata (DC.) Cov] vegetation. Sixteen plots (21.3×21.3 m) were laid out in four rows of four plots per row with a buffer zone of 7.6 m between plots and rows. A barbed wire fence excluded cattle and poultry wire fencing excluded lagomorphs. Treatments were factorially applied at two levels. Plant cover in the plots was sampled in 1938 (before treatment), 1947, 1956, 1960, 1967 and 1989 with randomly located, line-intercept transects. Data from all sampling dates were analyzed as a split plot in time and main effects for 1989 tested by analysis of variance for a 2×4 factorial experiment. There were significant (P<0.10) year x treatment interactions. Seeding and furrowing treatments were ineffective but lagomorph exclusion and shrub clearing treatments resulted in significant treatment differences for several species. In 1989, basal area of spike dropseed (Sporobolus contractus A.S. Hitchc.) was 30-fold greater on the lagomorph excluded than on the lagomorph unexcluded treatment. Canopy cover of honey mesquite (Prosopis glandulosa Torr. var. glandulosa), tarbush (Flourensia cernua DC.) and mariola (Parthenium incanum H.B.K.) were affected by lagomorph exclusion. None of the responses were viewed as successional in nature. They principally represented individual species sensitivities to either absence of a primary herbivore or removal of aboveground shrub biomass. Though the physical treatments could be regarded as relatively severe disturbances of the system, the impacts on community vegetation dynamics were relatively insignificant.