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.     

Recovery of tree and mammal communities during large‐scale forest regeneration in Kibale National Park,Uganda

Tropical landscapes are changing rapidly as a result of human modifications; however, despite increasing deforestation, human population growth, and the need for more agricultural land, deforestation rates have exceeded the rate at which land is converted to cropland or pasture. For deforested lands to have conservation value requires an understanding of regeneration rates of vegetation, the rates at which animals colonize and grow in regenerating areas, and the nature of interactions between plants and animals in the specific region. Here, we present data on forest regeneration and animal abundance at four regenerating sites that had reached the stage of closed canopy forest where the average dbh of the trees was 17 cm. Overall, 20.3 percent of stems were wind‐dispersed species and 79.7 percent were animal‐dispersed species, while in the old‐growth forest 17.3 percent of the stems were wind‐dispersed species. The regenerating forest supported a substantial primate population and encounter rate (groups per km walked) in the regenerating sites was high compared to the neighboring old‐growth forests. By monitoring elephant tracks for 10 yr, we demonstrated that elephant numbers increased steadily over time, but they increased dramatically since 2004. In general, the richness of the mammal community detected by sight, tracks, feces, and/or camera traps, was high in regenerating forests compared to that documented for the national park. We conclude that in Africa, a continent that has seen dramatic declines in the area of old‐growth forest, there is ample opportunity to reclaim degraded areas and quickly restore substantial animal populations.     

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.     

A novel regeneration system for a wild passion fruit species (<Emphasis Type="Italic">Passiflora cincinnata</Emphasis> Mast.) based on somatic embryogenesis from mature zygotic embryos

The objective of the present work was to induce somatic embryogenesis from zygotic embryos of Passiflora cincinnata Masters. Zygotic embryos formed calli on media with different concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D) and 4.5 μM benzyladenine (BA) after 30 days of in vitro culture. A concentration of 18.1 μM 2,4-D resulted in the largest number of somatic embryos. Embryogenic calli were yellowish and friable, forming whitish proembryogenic masses. Morphologically, embryogenic cells were small and had large nuclei and dense cytoplasm, whereas non-embryogenic cells were elongated, with small nuclei and less dense cytoplasm. Calli cultured under white light on basal Murashige and Skoog’s medium with activated charcoal produced embryos in all developmental stages. There were differences among the treatments, with some leading to the production of calli with embryos and some only to callus formation. Some abnormalities were associated with somatic embryos, including fused axes, fused cotyledons and polycotyledonary embryos. Production of secondary somatic embryos occurred in the first cycle of primary embryo development. Secondary embryos differentiated from the surface of the protodermal layer of primary embryos with intense cell proliferation, successive mitotic divisions in the initial phase of embryoid development, and a vascular system formed with no connection to the parental tissue. This secondary embryogenic system of P. cincinnata is characterized by intense proliferation and maintenance of embryogenic competence after successive subcultures. This reproducible protocol opens new prospects for massive propagation and is an alternative to the current organogenesis-based transformation protocol.     

Somatic embryogenesis from mature zygotic embryos of commercial passionfruit (<Emphasis Type="Italic">Passiflora edulis</Emphasis> Sims) genotypes

Mature zygotic embryos of three genotypes of Passiflora edulis Sims, including ‘FB-100’, ‘FB-200’, and ‘FB-300’ were incubated on a Murashige and Skoog (MS) (1962) medium supplemented with different concentrations (18.1–114.8 μM) of 2,4-diclorophenoxyacetic acid (2,4-D) and 4.4 μM of 6-benzyladenine (BA). MS basal medium and MS with BA induced germination of P. edulis embryos. The highest frequencies of embryogenic calli were observed when explants were incubated on MS medium supplemented with 72.4 μM 2,4-D and 4.4 μM BA for ‘FB-200’, which showed the highest potential for embryogenic callus formation. Cytological and histological analyses of pro-embryogenic callus revealed two distinct cell types: thin-walled, small, isodiametric cells with large nuclei and dense cytoplasm, typical of intense metabolic activity; and elongated and vacuolated cells, with small nuclei and less dense cytoplasm. Differentiation of somatic embryos was promoted on MS medium supplemented with activated charcoal and indole-3-acetyl-l-aspartic acid (IAA-Asp) either with or without 2,4-D. However, no conversion of somatic embryos into plantlets was observed.     

Carbohydrates as regulatory factors on the rooting of <Emphasis Type="Italic">Eucalyptus saligna</Emphasis> Smith and <Emphasis Type="Italic">Eucalyptus globulus</Emphasis> Labill

Comparisons between related species with different rooting capacities can provide insights into the mechanisms controlling adventitious root development. The availability of carbohydrates is often considered exclusively as an energetic requirement to drive root development; the major regulatory role in the process is often attributed to phytohormones, particularly auxin. The roles of light quantity (irradiance) and carbohydrate supply available to young aseptic donor-plants on the adventitious rooting response of Eucalyptus globulus (rooting recalcitrant) and Eucalyptus saligna (easy-to-root) were examined. The effects of the type of carbohydrate supply (sucrose or glucose) on the rooting response of cuttings was also evaluated. Light intensity supplied to mother-plants (30 or 60 mol m^–2 s^–1) had limited influence on the rooting response of both species, whereas dark periods were detrimental, particularly for E. globulus. In E. globulus, rooting was promoted by the absence of sucrose in donor-plant media. Presence of sucrose in donor plant medium promoted root number but did not affect rooting percentage of E. saligna. A positive effect of glucose on cutting rhizogenesis was found if this hexose was supplied during the root induction phase, followed by sucrose in the root formation step, especially for E. globulus. The same effect was not seen with fructose. The beneficial effect of glucose in the induction phase on root number was also evident under suboptimal auxin concentrations.     

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.     

Long‐term population monitoring of the threatened and endemic black‐headed squirrel monkey (Saimiri vanzolinii) shows the importance of protected areas for primate conservation in Amazonia

Population monitoring of endangered species is essential to the improvement of their management and conservation plans. The black‐headed squirrel monkey (Saimiri vanzolinii) is a vulnerable species on the IUCN Red List and has extreme geographical endemism, exhibiting the smallest known distribution among Neotropical primates (ca. 870 km²), over 90% of which occurs in white‐water flooded forests within the Mamirauá Sustainable Development Reserve (MSDR), Brazilian Amazonia. To assess the effectiveness of this protected area in conserving the species, we conducted population monitoring of black‐headed squirrel monkeys across five consecutive years (2009–2013) on nine trails 2 km each. Each year samples included both low and high river water periods. We used the distance sampling method, recording the distance to each observed social group as well as counting component individuals. We also calculated annual encounter rates based on the number of individuals sighted every 10 km traveled. Densities ranged from 256 individuals/km² (2011) to 453 individuals/km² (2013), and no seasonal differences were detected. Population size was estimated to be 147,848 mature individuals. Encounter rates ranged from 100 individuals/10 km (2010) to 179 individuals/10 km (2013); no significant difference among years was found. We found that S. vanzolinii populations remained stable throughout the years, which indicates that the MSDR has been playing an essential role on protecting this species. Due to difficulties of fulfilling assumptions of the distance sampling method, we consider the encounter rate analysis to be more effective for monitoring this and other Saimiri species. Given the critical endemism and worrying conservation status of S. vanzolinii, we suggest that monitoring of the species population should be carried out regularly.